rs2922997

Variant names:

• chr6-31369504-G-A
• rs2922997
• ENST00000649421.1: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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649421.1(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 ENST00000649421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000649421.1	n.274+2174G>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

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.555

Alfa AF: 0.555 Hom.: 4707

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2922997; hg19: chr6-31337281;