7-151898703-A-G

Variant names:

• chr7-151898703-A-G
• rs1109695

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 0.719 in 150,396 control chromosomes in the GnomAD database, including 40,018 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 0.72 (40018 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.720 AC: 108187 AN: 150282 Hom.: 40024 Cov.: 25

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.719 AC: 108206 AN: 150396 Hom.: 40018 Cov.: 25 AF XY: 0.712 AC XY: 52216 AN XY: 73298

African (AFR) AF: 0.576 AC: 23502 AN: 40780

American (AMR) AF: 0.624 AC: 9413 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2705 AN: 3462

East Asian (EAS) AF: 0.578 AC: 2913 AN: 5038

South Asian (SAS) AF: 0.672 AC: 3190 AN: 4750

European-Finnish (FIN) AF: 0.761 AC: 7756 AN: 10186

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56220 AN: 67794

Other (OTH) AF: 0.729 AC: 1524 AN: 2090

Alfa AF: 0.715 Hom.: 2341

Bravo AF: 0.700

Asia WGS AF: 0.609 AC: 2118 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.53
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1109695; hg19: chr7-151595788;