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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984214	XR_001747388.2	n.3189+6427T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304565	ENST00000804666.1	n.211+6427T>C		intron_variant	Intron 1 of 2
ENSG00000304565	ENST00000804667.1	n.255+6427T>C		intron_variant	Intron 1 of 1
ENSG00000304565	ENST00000804668.1	n.*177T>C		downstream_gene_variant

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 v4.3

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

Other links and lift over

dbSNP: rs7072776; hg19: chr10-22032942;