chr5-7934537-A-G

Variant names:

• chr5-7934537-A-G
• rs10512932

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 0.193 in 152,240 control chromosomes in the GnomAD database, including 3,008 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 0.19 (3008 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.358 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: 0.193 AC: 29349 AN: 152122 Hom.: 3007 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.193 AC: 29357 AN: 152240 Hom.: 3008 Cov.: 32 AF XY: 0.194 AC XY: 14418 AN XY: 74428

African (AFR) AF: 0.165 AC: 6849 AN: 41558

American (AMR) AF: 0.181 AC: 2759 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3466

East Asian (EAS) AF: 0.153 AC: 794 AN: 5180

South Asian (SAS) AF: 0.373 AC: 1798 AN: 4824

European-Finnish (FIN) AF: 0.156 AC: 1653 AN: 10594

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13716 AN: 68014

Other (OTH) AF: 0.244 AC: 517 AN: 2116

Alfa AF: 0.193 Hom.: 394

Bravo AF: 0.189

Asia WGS AF: 0.286 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.55
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10512932; hg19: chr5-7934650;