rs7919724

Variant names:

• chr10-60736084-G-A
• rs7919724
• ENST00000517854.1:n.87+1656G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-60736084-G-A
• chr10-60736084-G-T

Variant summary

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

The ENST00000517854.1(ANK3-DT):​n.87+1656G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,014 control chromosomes in the GnomAD database, including 33,744 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 0.66 (33744 hom., cov: 32)
• Consequence: ANK3-DT ENST00000517854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 6 publications found

Genes affected

ANK3-DT (HGNC:54102): (ANK3 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517854.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANK3-DT	NR_184155.1		n.172+1656G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANK3-DT	ENST00000517854.1	TSL:3	n.87+1656G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101012 AN: 151896 Hom.: 33715 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.665 AC: 101088 AN: 152014 Hom.: 33744 Cov.: 32 AF XY: 0.670 AC XY: 49769 AN XY: 74328

African (AFR) AF: 0.631 AC: 26153 AN: 41444

American (AMR) AF: 0.698 AC: 10677 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2637 AN: 3470

East Asian (EAS) AF: 0.569 AC: 2935 AN: 5162

South Asian (SAS) AF: 0.797 AC: 3842 AN: 4820

European-Finnish (FIN) AF: 0.679 AC: 7163 AN: 10550

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45418 AN: 67966

Other (OTH) AF: 0.669 AC: 1411 AN: 2110

Alfa AF: 0.672 Hom.: 54404

Bravo AF: 0.659

Asia WGS AF: 0.689 AC: 2390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.73
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs7919724; hg19: chr10-62495842;