rs1617640

Positions:

• 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: intergenic_region
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -2.46

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.100719675C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

risk factor, no assertion criteria provided

literature only

OMIM

May 13, 2008

- -

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;