rs2922997

Variant names:

• chr6-31369504-G-A
• rs2922997
• ENST00000649421.2:n.274+2174G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31369504-G-A
• chr6-31369504-G-T

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.274+2174G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,190 control chromosomes in the GnomAD database, including 22,278 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 0.54 (22278 hom., cov: 33)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879
• Publications: 7 publications found

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 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
ENSG00000285647	ENST00000649421.2	n.274+2174G>A		intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1	n.327-12476G>A		intron_variant	Intron 1 of 1
ENSG00000285647	ENST00000755530.1	n.203-5379G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81707 AN: 152072 Hom.: 22272 Cov.: 33

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.537 AC: 81745 AN: 152190 Hom.: 22278 Cov.: 33 AF XY: 0.532 AC XY: 39619 AN XY: 74406

African (AFR) AF: 0.488 AC: 20282 AN: 41526

American (AMR) AF: 0.479 AC: 7332 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1365 AN: 3472

East Asian (EAS) AF: 0.611 AC: 3168 AN: 5188

South Asian (SAS) AF: 0.572 AC: 2760 AN: 4824

European-Finnish (FIN) AF: 0.478 AC: 5059 AN: 10580

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.587 AC: 39914 AN: 67990

Other (OTH) AF: 0.555 AC: 1172 AN: 2112

Alfa AF: 0.553 Hom.: 5799

Bravo AF: 0.536

Asia WGS AF: 0.550 AC: 1912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.39
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2922997; hg19: chr6-31337281;