17-37672843-A-G

Variant names:

• chr17-37672843-A-G
• rs1859212
• ENST00000613901.1:n.109-2981A>G

Variant summary

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

The ENST00000613901.1(ENSG00000277688):​n.109-2981A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,080 control chromosomes in the GnomAD database, including 32,842 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 0.64 (32842 hom., cov: 32)
• Consequence: ENSG00000277688 ENST00000613901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664
• Publications: 4 publications found

Genes affected

ENSG00000277688 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000613901.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000277688	ENST00000613901.1	TSL:4	n.109-2981A>G		intron	N/A
	ENSG00000277688	ENST00000615265.1	TSL:3	n.591-11372A>G		intron	N/A
	ENSG00000277688	ENST00000717157.1		n.430+7303A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96930 AN: 151962 Hom.: 32784 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.638 AC: 97057 AN: 152080 Hom.: 32842 Cov.: 32 AF XY: 0.635 AC XY: 47187 AN XY: 74334

African (AFR) AF: 0.885 AC: 36732 AN: 41516

American (AMR) AF: 0.563 AC: 8605 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2177 AN: 3468

East Asian (EAS) AF: 0.485 AC: 2497 AN: 5152

South Asian (SAS) AF: 0.672 AC: 3237 AN: 4816

European-Finnish (FIN) AF: 0.488 AC: 5154 AN: 10562

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36735 AN: 67974

Other (OTH) AF: 0.630 AC: 1332 AN: 2114

Alfa AF: 0.589 Hom.: 9860

Bravo AF: 0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.2
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs1859212; hg19: chr17-36032844;