chr2-83722614-A-G

Variant names:

• chr2-83722614-A-G
• rs972021
• ENST00000836511.1:n.147-8462A>G

Variant summary

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

The ENST00000836511.1(ENSG00000308806):​n.147-8462A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 151,982 control chromosomes in the GnomAD database, including 70,402 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 0.96 (70402 hom., cov: 30)
• Consequence: ENSG00000308806 ENST00000836511.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 1 publications found

Genes affected

ENSG00000308806 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836511.1. 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
	ENSG00000308806	ENST00000836511.1		n.147-8462A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146096 AN: 151864 Hom.: 70366 Cov.: 30

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.962 AC: 146187 AN: 151982 Hom.: 70402 Cov.: 30 AF XY: 0.961 AC XY: 71384 AN XY: 74316

African (AFR) AF: 0.916 AC: 37994 AN: 41480

American (AMR) AF: 0.981 AC: 14941 AN: 15238

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3469 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5110 AN: 5128

South Asian (SAS) AF: 0.887 AC: 4282 AN: 4828

European-Finnish (FIN) AF: 0.975 AC: 10340 AN: 10600

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.984 AC: 66822 AN: 67920

Other (OTH) AF: 0.970 AC: 2048 AN: 2112

Alfa AF: 0.975 Hom.: 28104

Bravo AF: 0.963

Asia WGS AF: 0.926 AC: 3220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.48
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs972021; hg19: chr2-83949738;