rs2395670

Variant names:

• chr6-37115033-A-G
• rs2395670
• ENST00000739933.1:n.295+1626T>C

Variant summary

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

The ENST00000739933.1(ENSG00000296499):​n.295+1626T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 151,950 control chromosomes in the GnomAD database, including 36,839 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 0.69 (36839 hom., cov: 30)
• Consequence: ENSG00000296499 ENST00000739933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 9 publications found

Genes affected

ENSG00000296499 (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 = 0.863 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739933.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296499	ENST00000739933.1		n.295+1626T>C		intron	N/A
	ENSG00000296499	ENST00000739934.1		n.327+1626T>C		intron	N/A
	ENSG00000296499	ENST00000739935.1		n.133+22629T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105335 AN: 151832 Hom.: 36788 Cov.: 30

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.694 AC: 105451 AN: 151950 Hom.: 36839 Cov.: 30 AF XY: 0.696 AC XY: 51642 AN XY: 74242

African (AFR) AF: 0.708 AC: 29346 AN: 41438

American (AMR) AF: 0.716 AC: 10921 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2499 AN: 3472

East Asian (EAS) AF: 0.885 AC: 4584 AN: 5182

South Asian (SAS) AF: 0.771 AC: 3714 AN: 4814

European-Finnish (FIN) AF: 0.609 AC: 6414 AN: 10528

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45528 AN: 67940

Other (OTH) AF: 0.724 AC: 1531 AN: 2116

Alfa AF: 0.679 Hom.: 152192

Bravo AF: 0.701

Asia WGS AF: 0.796 AC: 2772 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	3.7
DANN	Benign	0.54
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2395670; hg19: chr6-37082809;