10-21744013-A-G

Variant names:

• chr10-21744013-A-G
• rs7072776
• ENST00000804666.1:n.211+6427T>C

Variant summary

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

The ENST00000804666.1(ENSG00000304565):​n.211+6427T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,102 control chromosomes in the GnomAD database, including 33,762 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 (33762 hom., cov: 32)
• Consequence: ENSG00000304565 ENST00000804666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• Publications: 83 publications found

Genes affected

ENSG00000304565 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804666.1. 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
	ENSG00000304565	ENST00000804666.1		n.211+6427T>C		intron	N/A
	ENSG00000304565	ENST00000804667.1		n.255+6427T>C		intron	N/A
	ENSG00000304565	ENST00000804668.1		n.*177T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99652 AN: 151984 Hom.: 33765 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.655 AC: 99666 AN: 152102 Hom.: 33762 Cov.: 32 AF XY: 0.661 AC XY: 49168 AN XY: 74346

African (AFR) AF: 0.492 AC: 20381 AN: 41440

American (AMR) AF: 0.645 AC: 9869 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2140 AN: 3470

East Asian (EAS) AF: 0.951 AC: 4930 AN: 5186

South Asian (SAS) AF: 0.792 AC: 3804 AN: 4806

European-Finnish (FIN) AF: 0.766 AC: 8109 AN: 10580

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48495 AN: 68000

Other (OTH) AF: 0.629 AC: 1330 AN: 2114

Alfa AF: 0.691 Hom.: 129649

Bravo AF: 0.640

Asia WGS AF: 0.790 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.76
PhyloP100		-0.40

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: rs7072776;

hg19: chr10-22032942;