rs1229540

Variant names:

• chr7-97794082-G-A
• rs1229540

Your query was ambiguous. Multiple possible variants found:

• chr7-97794082-G-A
• chr7-97794082-G-C
• chr7-97794082-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 0.633 in 151,898 control chromosomes in the GnomAD database, including 31,100 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 0.63 (31100 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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: 0.633 AC: 96069 AN: 151780 Hom.: 31060 Cov.: 33

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.633 AC: 96166 AN: 151898 Hom.: 31100 Cov.: 33 AF XY: 0.632 AC XY: 46893 AN XY: 74248

African (AFR) AF: 0.769 AC: 31874 AN: 41426

American (AMR) AF: 0.660 AC: 10063 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2062 AN: 3462

East Asian (EAS) AF: 0.671 AC: 3473 AN: 5172

South Asian (SAS) AF: 0.636 AC: 3061 AN: 4816

European-Finnish (FIN) AF: 0.556 AC: 5870 AN: 10556

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37742 AN: 67908

Other (OTH) AF: 0.629 AC: 1321 AN: 2100

Alfa AF: 0.574 Hom.: 27359

Bravo AF: 0.651

Asia WGS AF: 0.658 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.35
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs1229540; hg19: chr7-97423394;