rs7787163

Variant names:

• chr7-89538067-C-A
• rs7787163

Your query was ambiguous. Multiple possible variants found:

• chr7-89538067-C-A
• chr7-89538067-C-T

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 0.148 in 151,938 control chromosomes in the GnomAD database, including 1,815 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 0.15 (1815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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: 0.148 AC: 22511 AN: 151822 Hom.: 1810 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0972

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.148 AC: 22549 AN: 151938 Hom.: 1815 Cov.: 32 AF XY: 0.145 AC XY: 10732 AN XY: 74254

African (AFR) AF: 0.202 AC: 8387 AN: 41472

American (AMR) AF: 0.146 AC: 2227 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3468

East Asian (EAS) AF: 0.0969 AC: 500 AN: 5162

South Asian (SAS) AF: 0.0970 AC: 467 AN: 4816

European-Finnish (FIN) AF: 0.0851 AC: 896 AN: 10528

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8867 AN: 67934

Other (OTH) AF: 0.148 AC: 311 AN: 2108

Alfa AF: 0.102 Hom.: 261

Bravo AF: 0.159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.8
DANN	Benign	0.73
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs7787163; hg19: chr7-89167381; COSMIC: COSV50193138;