rs7211602

Positions:

• chr17-37666371-A-C

Variant summary

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

The variant allele was found at a frequency of 0.684 in 152,172 control chromosomes in the GnomAD database, including 36,953 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 0.68 (36953 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37666371A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000277501	ENST00000613901.1	n.109-9453A>C		intron_variant		4
ENSG00000277501	ENST00000615265.1	n.591-17844A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103975 AN: 152054 Hom.: 36880 Cov.: 33

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.684 AC: 104106 AN: 152172 Hom.: 36953 Cov.: 33 AF XY: 0.684 AC XY: 50848 AN XY: 74392

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.659

Alfa AF: 0.612 Hom.: 33717

Bravo AF: 0.706

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7211602; hg19: chr17-36026401;