1-173668379-A-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ENSG00000285777 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198493.3. 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
	ANKRD45	NM_198493.3	MANE Select	c.-16+1438T>A		intron	N/A	NP_940895.1	Q5TZF3-2
	ANKRD45	NR_158771.1		n.35+1438T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD45	ENST00000333279.3	TSL:1 MANE Select	c.-16+1438T>A		intron	N/A	ENSP00000331268.2	Q5TZF3-2
	ANKRD45	ENST00000367712.2	TSL:1	n.16+1438T>A		intron	N/A
	ENSG00000285777	ENST00000648193.1		n.-16+1438T>A		intron	N/A	ENSP00000498204.1

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

African (AFR) AF: 0.751 AC: 31143 AN: 41450

American (AMR) AF: 0.313 AC: 4778 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1520 AN: 3468

East Asian (EAS) AF: 0.605 AC: 3129 AN: 5168

South Asian (SAS) AF: 0.228 AC: 1097 AN: 4810

European-Finnish (FIN) AF: 0.224 AC: 2374 AN: 10588

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19347 AN: 67978

Other (OTH) AF: 0.389 AC: 823 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.99
DANN	Benign	0.75
PhyloP100		-0.49
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: rs10912660; hg19: chr1-173637518;