rs7211602

Variant names:

• chr17-37666371-A-C
• rs7211602
• ENST00000613901.1:n.109-9453A>C

Variant summary

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

The ENST00000615265.1(ENSG00000277688):​n.591-17844A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000277688 ENST00000615265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615265.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000277688	ENST00000613901.1	TSL:4	n.109-9453A>C		intron	N/A
	ENSG00000277688	ENST00000615265.1	TSL:3	n.591-17844A>C		intron	N/A
	ENSG00000277688	ENST00000717157.1		n.430+831A>C		intron	N/A

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

African (AFR) AF: 0.879 AC: 36506 AN: 41554

American (AMR) AF: 0.716 AC: 10947 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2019 AN: 3464

East Asian (EAS) AF: 0.728 AC: 3767 AN: 5172

South Asian (SAS) AF: 0.709 AC: 3421 AN: 4826

European-Finnish (FIN) AF: 0.558 AC: 5894 AN: 10570

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39621 AN: 67986

Other (OTH) AF: 0.659 AC: 1394 AN: 2114

Alfa AF: 0.625 Hom.: 96284

Bravo AF: 0.706

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs7211602; hg19: chr17-36026401;