rs288746

Variant names:

• chr7-155813978-G-A
• rs288746

Your query was ambiguous. Multiple possible variants found:

• chr7-155813978-G-A
• chr7-155813978-G-C
• chr7-155813978-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 0.873 in 152,108 control chromosomes in the GnomAD database, including 58,089 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 0.87 (58089 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 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: 0.873 AC: 132646 AN: 151992 Hom.: 58031 Cov.: 30

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.984

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.873 AC: 132764 AN: 152108 Hom.: 58089 Cov.: 30 AF XY: 0.873 AC XY: 64909 AN XY: 74352

African (AFR) AF: 0.839 AC: 34811 AN: 41496

American (AMR) AF: 0.879 AC: 13432 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3045 AN: 3466

East Asian (EAS) AF: 0.982 AC: 5050 AN: 5142

South Asian (SAS) AF: 0.924 AC: 4450 AN: 4814

European-Finnish (FIN) AF: 0.870 AC: 9216 AN: 10590

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59817 AN: 68004

Other (OTH) AF: 0.863 AC: 1821 AN: 2110

Alfa AF: 0.874 Hom.: 187370

Bravo AF: 0.872

Asia WGS AF: 0.944 AC: 3282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.066
DANN	Benign	0.70
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs288746; hg19: chr7-155606672;