rs2249741

Variant names:

• chr6-31272935-A-C
• rs2249741
• ENST00000755297.1:n.32+1829A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-31272935-A-C
• chr6-31272935-A-T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+1829A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,648 control chromosomes in the GnomAD database, including 26,135 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 0.58 (26135 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 11 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. 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
	ENSG00000298396	ENST00000755297.1		n.32+1829A>C		intron	N/A
	ENSG00000288813	ENST00000692808.2		n.*66A>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88357 AN: 151530 Hom.: 26114 Cov.: 31

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.724

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.583 AC: 88423 AN: 151648 Hom.: 26135 Cov.: 31 AF XY: 0.585 AC XY: 43358 AN XY: 74136

African (AFR) AF: 0.648 AC: 26778 AN: 41326

American (AMR) AF: 0.612 AC: 9327 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2820 AN: 3464

East Asian (EAS) AF: 0.564 AC: 2906 AN: 5148

South Asian (SAS) AF: 0.684 AC: 3292 AN: 4816

European-Finnish (FIN) AF: 0.504 AC: 5297 AN: 10502

Middle Eastern (MID) AF: 0.717 AC: 208 AN: 290

European-Non Finnish (NFE) AF: 0.529 AC: 35889 AN: 67844

Other (OTH) AF: 0.651 AC: 1372 AN: 2108

Alfa AF: 0.548 Hom.: 9964

Bravo AF: 0.594

Asia WGS AF: 0.609 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.8
DANN	Benign	0.41
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2249741; hg19: chr6-31240712;