chr7-21152762-C-A

Variant names:

• chr7-21152762-C-A
• rs7792457
• ENST00000821909.1:n.382+9399G>T

Variant summary

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

The ENST00000821909.1(ENSG00000306908):​n.382+9399G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 151,892 control chromosomes in the GnomAD database, including 1,528 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 0.12 (1528 hom., cov: 32)
• Consequence: ENSG00000306908 ENST00000821909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 1 publications found

Genes affected

ENSG00000306908 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306908	ENST00000821909.1	n.382+9399G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18390 AN: 151774 Hom.: 1526 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0397

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.121 AC: 18408 AN: 151892 Hom.: 1528 Cov.: 32 AF XY: 0.117 AC XY: 8654 AN XY: 74212

African (AFR) AF: 0.232 AC: 9591 AN: 41370

American (AMR) AF: 0.0808 AC: 1231 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0905 AC: 314 AN: 3468

East Asian (EAS) AF: 0.151 AC: 782 AN: 5172

South Asian (SAS) AF: 0.0396 AC: 190 AN: 4802

European-Finnish (FIN) AF: 0.0414 AC: 437 AN: 10558

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0821 AC: 5580 AN: 67968

Other (OTH) AF: 0.104 AC: 220 AN: 2108

Alfa AF: 0.0888 Hom.: 356

Bravo AF: 0.129

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.30
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs7792457; hg19: chr7-21192381;