rs10264893

Variant names:

• chr7-104013977-G-A
• rs10264893
• ENST00000776085.1:n.107-11880C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-104013977-G-A
• chr7-104013977-G-T

Variant summary

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

The ENST00000776085.1(ENSG00000301094):​n.107-11880C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,946 control chromosomes in the GnomAD database, including 17,488 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 0.48 (17488 hom., cov: 32)
• Consequence: ENSG00000301094 ENST00000776085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 2 publications found

Genes affected

ENSG00000301094 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776085.1. 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
	ENSG00000301094	ENST00000776085.1		n.107-11880C>T		intron	N/A
	ENSG00000301094	ENST00000776086.1		n.111-8168C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72166 AN: 151828 Hom.: 17480 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.475 AC: 72215 AN: 151946 Hom.: 17488 Cov.: 32 AF XY: 0.485 AC XY: 36055 AN XY: 74268

African (AFR) AF: 0.466 AC: 19312 AN: 41464

American (AMR) AF: 0.522 AC: 7957 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1514 AN: 3464

East Asian (EAS) AF: 0.750 AC: 3875 AN: 5170

South Asian (SAS) AF: 0.547 AC: 2638 AN: 4822

European-Finnish (FIN) AF: 0.534 AC: 5635 AN: 10556

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29712 AN: 67922

Other (OTH) AF: 0.487 AC: 1028 AN: 2110

Alfa AF: 0.440 Hom.: 11015

Bravo AF: 0.472

Asia WGS AF: 0.601 AC: 2094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.44
PhyloP100		-0.0030

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: rs10264893;

hg19: chr7-103654424;