ENST00000821909.1:n.383-4370G>A

Variant names:

• chr7-21123736-C-T
• rs10950840
• ENST00000821909.1:n.383-4370G>A

Variant summary

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

The ENST00000821909.1(ENSG00000306908):​n.383-4370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,028 control chromosomes in the GnomAD database, including 44,093 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 0.76 (44093 hom., cov: 31)
• Consequence: ENSG00000306908 ENST00000821909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 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.383-4370G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115614 AN: 151910 Hom.: 44055 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.761 AC: 115707 AN: 152028 Hom.: 44093 Cov.: 31 AF XY: 0.763 AC XY: 56690 AN XY: 74318

African (AFR) AF: 0.780 AC: 32334 AN: 41458

American (AMR) AF: 0.779 AC: 11904 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2484 AN: 3470

East Asian (EAS) AF: 0.757 AC: 3911 AN: 5164

South Asian (SAS) AF: 0.683 AC: 3289 AN: 4814

European-Finnish (FIN) AF: 0.803 AC: 8496 AN: 10576

Middle Eastern (MID) AF: 0.707 AC: 205 AN: 290

European-Non Finnish (NFE) AF: 0.747 AC: 50801 AN: 67962

Other (OTH) AF: 0.750 AC: 1585 AN: 2114

Alfa AF: 0.749 Hom.: 122861

Bravo AF: 0.760

Asia WGS AF: 0.728 AC: 2535 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	11
DANN	Benign	0.66
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs10950840; hg19: chr7-21163355;