1-173668379-A-T

Variant names:

• chr1-173668379-A-T
• rs10912660
• NM_198493.3:c.-16+1438T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198493.3(ANKRD45):​c.-16+1438T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,064 control chromosomes in the GnomAD database, including 17,283 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 0.42 (17283 hom., cov: 32)
• Consequence: ANKRD45 NM_198493.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

Genes affected

ANKRD45 (HGNC:24786): (ankyrin repeat domain 45)

ENSG00000285777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD45	NM_198493.3	c.-16+1438T>A		intron_variant	Intron 1 of 5	ENST00000333279.3	NP_940895.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD45	ENST00000333279.3	c.-16+1438T>A		intron_variant	Intron 1 of 5	1	NM_198493.3	ENSP00000331268.2
ANKRD45	ENST00000367712.2	n.16+1438T>A		intron_variant	Intron 1 of 1	1
ENSG00000285777	ENST00000648193.1	n.-16+1438T>A		intron_variant	Intron 1 of 7			ENSP00000498204.1
ENSG00000289426	ENST00000693292.1	n.323-2855A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64463 AN: 151946 Hom.: 17223 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.387

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.425 AC: 64584 AN: 152064 Hom.: 17283 Cov.: 32 AF XY: 0.418 AC XY: 31112 AN XY: 74346

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.389

Alfa AF: 0.353 Hom.: 1409

Bravo AF: 0.448

Asia WGS AF: 0.443 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.99
DANN	Benign	0.75

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

Publications

LitVar

Other links and lift over

dbSNP: rs10912660; hg19: chr1-173637518;