chr7-7617673-C-T

Variant names:

• chr7-7617673-C-T
• rs1557996

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 0.786 in 152,098 control chromosomes in the GnomAD database, including 47,984 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 0.79 (47984 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119414 AN: 151980 Hom.: 47963 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.786 AC: 119486 AN: 152098 Hom.: 47984 Cov.: 31 AF XY: 0.789 AC XY: 58688 AN XY: 74336

African (AFR) AF: 0.597 AC: 24732 AN: 41460

American (AMR) AF: 0.852 AC: 13009 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2970 AN: 3468

East Asian (EAS) AF: 0.937 AC: 4846 AN: 5174

South Asian (SAS) AF: 0.796 AC: 3845 AN: 4828

European-Finnish (FIN) AF: 0.883 AC: 9346 AN: 10580

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 57994 AN: 68000

Other (OTH) AF: 0.797 AC: 1683 AN: 2112

Alfa AF: 0.830 Hom.: 90176

Bravo AF: 0.777

Asia WGS AF: 0.818 AC: 2845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.78
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1557996; hg19: chr7-7657304;