rs1689198

Variant names:

• chr7-156244652-G-A
• rs1689198

Your query was ambiguous. Multiple possible variants found:

• chr7-156244652-G-A
• chr7-156244652-G-C
• chr7-156244652-G-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 0.564 in 151,212 control chromosomes in the GnomAD database, including 24,159 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 0.56 (24159 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.618 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: 0.564 AC: 85232 AN: 151094 Hom.: 24148 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.564 AC: 85286 AN: 151212 Hom.: 24159 Cov.: 32 AF XY: 0.566 AC XY: 41788 AN XY: 73840

African (AFR) AF: 0.541 AC: 22318 AN: 41236

American (AMR) AF: 0.629 AC: 9577 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2446 AN: 3446

East Asian (EAS) AF: 0.587 AC: 3018 AN: 5142

South Asian (SAS) AF: 0.498 AC: 2392 AN: 4800

European-Finnish (FIN) AF: 0.601 AC: 6278 AN: 10446

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.552 AC: 37343 AN: 67606

Other (OTH) AF: 0.575 AC: 1207 AN: 2100

Alfa AF: 0.547 Hom.: 2665

Bravo AF: 0.569

Asia WGS AF: 0.512 AC: 1777 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.9
DANN	Benign	0.72
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1689198; hg19: chr7-156037346;