chr7-100719675-C-A

Variant names:

• chr7-100719675-C-A
• rs1617640

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 87 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.656 AC: 27150 AN: 41410

American (AMR) AF: 0.718 AC: 10946 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2475 AN: 3472

East Asian (EAS) AF: 0.805 AC: 4154 AN: 5162

South Asian (SAS) AF: 0.643 AC: 3095 AN: 4814

European-Finnish (FIN) AF: 0.526 AC: 5547 AN: 10538

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40514 AN: 67962

Other (OTH) AF: 0.676 AC: 1415 AN: 2094

Alfa AF: 0.614 Hom.: 47684

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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.11
DANN	Benign	0.42
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1617640; hg19: chr7-100317298;