rs2844619

Variant names:

• chr6-31274446-C-G
• rs2844619
• ENST00000755297.1:n.32+3340C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-31274446-C-G
• chr6-31274446-C-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+3340C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 150,490 control chromosomes in the GnomAD database, including 32,728 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 0.66 (32728 hom., cov: 27)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 17 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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
ENSG00000298396	ENST00000755297.1	n.32+3340C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.660 AC: 99189 AN: 150378 Hom.: 32710 Cov.: 27

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.660 AC: 99249 AN: 150490 Hom.: 32728 Cov.: 27 AF XY: 0.665 AC XY: 48869 AN XY: 73522

African (AFR) AF: 0.658 AC: 26848 AN: 40780

American (AMR) AF: 0.718 AC: 10893 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2794 AN: 3462

East Asian (EAS) AF: 0.808 AC: 4140 AN: 5126

South Asian (SAS) AF: 0.748 AC: 3554 AN: 4752

European-Finnish (FIN) AF: 0.659 AC: 6828 AN: 10360

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 41960 AN: 67562

Other (OTH) AF: 0.693 AC: 1442 AN: 2082

Alfa AF: 0.476 Hom.: 1197

Bravo AF: 0.657

Asia WGS AF: 0.744 AC: 2591 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	3.3
DANN	Benign	0.49
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs2844619; hg19: chr6-31242223;