17-37672843-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000615265.1(ENSG00000277501):​n.591-11372A>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: ENSG00000277501 ENST00000615265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664

Genes affected

ENSG00000277501 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000277501	ENST00000613901.1	n.109-2981A>G		intron_variant	Intron 1 of 1	4
ENSG00000277501	ENST00000615265.1	n.591-11372A>G		intron_variant	Intron 1 of 1	3

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

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.630

Alfa AF: 0.587 Hom.: 5284

Bravo AF: 0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1859212; hg19: chr17-36032844;