rs727505

Variant names:

• chr7-124822027-G-A
• rs727505

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 0.232 in 151,870 control chromosomes in the GnomAD database, including 4,358 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 0.23 (4358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 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: 0.233 AC: 35290 AN: 151752 Hom.: 4355 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.232 AC: 35308 AN: 151870 Hom.: 4358 Cov.: 32 AF XY: 0.228 AC XY: 16907 AN XY: 74204

African (AFR) AF: 0.162 AC: 6701 AN: 41488

American (AMR) AF: 0.200 AC: 3045 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3464

East Asian (EAS) AF: 0.303 AC: 1553 AN: 5132

South Asian (SAS) AF: 0.185 AC: 889 AN: 4818

European-Finnish (FIN) AF: 0.201 AC: 2116 AN: 10552

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19250 AN: 67844

Other (OTH) AF: 0.223 AC: 471 AN: 2114

Alfa AF: 0.268 Hom.: 12500

Bravo AF: 0.231

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.54
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs727505; hg19: chr7-124462081;