rs3091367

Variant names:

• chr22-37831814-C-G
• rs3091367
• NM_138797.4:c.*129G>C

Your query was ambiguous. Multiple possible variants found:

• chr22-37831814-C-G
• chr22-37831814-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138797.4(ANKRD54):​c.*129G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 890,492 control chromosomes in the GnomAD database, including 27,556 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.27 (5900 hom., cov: 33)
  • Exomes 𝑓: 0.24 (21656 hom.)
• Consequence: ANKRD54 NM_138797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 5 publications found

Genes affected

ANKRD54 (HGNC:25185): (ankyrin repeat domain 54) Predicted to enable protein kinase regulator activity. Predicted to be involved in positive regulation of erythrocyte differentiation; regulation of intracellular signal transduction; and regulation of protein kinase activity. Predicted to act upstream of or within nucleocytoplasmic transport. Predicted to be located in midbody. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138797.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD54	NM_138797.4	MANE Select	c.*129G>C		3_prime_UTR	Exon 8 of 8	NP_620152.1	Q6NXT1-1
	ANKRD54	NM_001349853.2		c.*129G>C		3_prime_UTR	Exon 8 of 8	NP_001336782.1
	ANKRD54	NM_001363839.1		c.*129G>C		3_prime_UTR	Exon 8 of 8	NP_001350768.1	B5MCX7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD54	ENST00000215941.9	TSL:1 MANE Select	c.*129G>C		3_prime_UTR	Exon 8 of 8	ENSP00000215941.4	Q6NXT1-1
	ANKRD54	ENST00000873384.1		c.*129G>C		3_prime_UTR	Exon 8 of 8	ENSP00000543443.1
	ANKRD54	ENST00000957324.1		c.*129G>C		3_prime_UTR	Exon 7 of 7	ENSP00000627383.1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41313 AN: 152034 Hom.: 5901 Cov.: 33

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.0975

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.285

GnomAD4 exome AF: 0.236 AC: 174555 AN: 738340 Hom.: 21656 Cov.: 10 AF XY: 0.237 AC XY: 88783 AN XY: 375242

African (AFR) AF: 0.359 AC: 6642 AN: 18496

American (AMR) AF: 0.301 AC: 7497 AN: 24924

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 4151 AN: 16194

East Asian (EAS) AF: 0.0700 AC: 2262 AN: 32312

South Asian (SAS) AF: 0.222 AC: 12260 AN: 55304

European-Finnish (FIN) AF: 0.250 AC: 8032 AN: 32106

Middle Eastern (MID) AF: 0.313 AC: 1276 AN: 4082

European-Non Finnish (NFE) AF: 0.238 AC: 123600 AN: 519404

Other (OTH) AF: 0.249 AC: 8835 AN: 35518

GnomAD4 genome AF: 0.272 AC: 41342 AN: 152152 Hom.: 5900 Cov.: 33 AF XY: 0.268 AC XY: 19966 AN XY: 74368

African (AFR) AF: 0.350 AC: 14537 AN: 41524

American (AMR) AF: 0.300 AC: 4592 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 904 AN: 3472

East Asian (EAS) AF: 0.0975 AC: 505 AN: 5178

South Asian (SAS) AF: 0.200 AC: 965 AN: 4816

European-Finnish (FIN) AF: 0.248 AC: 2627 AN: 10572

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16243 AN: 67984

Other (OTH) AF: 0.281 AC: 595 AN: 2116

Alfa AF: 0.141 Hom.: 248

Bravo AF: 0.281

Asia WGS AF: 0.166 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.55
PhyloP100		1.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3091367; hg19: chr22-38227821; COSMIC: COSV53236495; COSMIC: COSV53236495;