10-93724962-G-A

Variant names:

• chr10-93724962-G-A
• rs1339577
• ENST00000793614.1:n.1220-12596C>T

Variant summary

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

The ENST00000793614.1(ENSG00000303320):​n.1220-12596C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 151,486 control chromosomes in the GnomAD database, including 48,520 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 0.80 (48520 hom., cov: 33)
• Consequence: ENSG00000303320 ENST00000793614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 1 publications found

Genes affected

ENSG00000303320 (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 (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793614.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303320	ENST00000793614.1		n.1220-12596C>T		intron	N/A
	ENSG00000303320	ENST00000793615.1		n.303-12596C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121060 AN: 151366 Hom.: 48483 Cov.: 33

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.800 AC: 121154 AN: 151486 Hom.: 48520 Cov.: 33 AF XY: 0.797 AC XY: 58984 AN XY: 74012

African (AFR) AF: 0.816 AC: 33730 AN: 41312

American (AMR) AF: 0.747 AC: 11375 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2942 AN: 3458

East Asian (EAS) AF: 0.932 AC: 4809 AN: 5160

South Asian (SAS) AF: 0.800 AC: 3852 AN: 4812

European-Finnish (FIN) AF: 0.766 AC: 8044 AN: 10496

Middle Eastern (MID) AF: 0.862 AC: 250 AN: 290

European-Non Finnish (NFE) AF: 0.793 AC: 53678 AN: 67720

Other (OTH) AF: 0.799 AC: 1685 AN: 2108

Alfa AF: 0.797 Hom.: 69856

Bravo AF: 0.802

Asia WGS AF: 0.866 AC: 3010 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	0.12
DANN	Benign	0.39
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1339577;

hg19: chr10-95484719;