rs1617640

Variant names:

• chr7-100719675-C-A
• rs1617640

Your query was ambiguous. Multiple possible variants found:

• chr7-100719675-C-A
• chr7-100719675-C-G
• chr7-100719675-C-T

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 0.632 in 151,908 control chromosomes in the GnomAD database, including 30,572 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.63 (30572 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -2.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 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

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95880 AN: 151790 Hom.: 30553 Cov.: 31

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.632 AC: 95943 AN: 151908 Hom.: 30572 Cov.: 31 AF XY: 0.635 AC XY: 47144 AN XY: 74234

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.676

Alfa AF: 0.556 Hom.: 3685

Bravo AF: 0.646

Asia WGS AF: 0.703 AC: 2447 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Microvascular complications of diabetes, susceptibility to, 2 Other:1

May 13, 2008

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.11
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1617640; hg19: chr7-100317298;