5-7936174-T-C

Variant names:

• chr5-7936174-T-C
• rs10512934

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 152,186 control chromosomes in the GnomAD database, including 3,006 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 (3006 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 3 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 (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: 29338 AN: 152068 Hom.: 3005 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.193 AC: 29346 AN: 152186 Hom.: 3006 Cov.: 33 AF XY: 0.194 AC XY: 14421 AN XY: 74424

African (AFR) AF: 0.165 AC: 6836 AN: 41520

American (AMR) AF: 0.180 AC: 2754 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3468

East Asian (EAS) AF: 0.153 AC: 793 AN: 5182

South Asian (SAS) AF: 0.372 AC: 1797 AN: 4826

European-Finnish (FIN) AF: 0.157 AC: 1661 AN: 10596

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

European-Non Finnish (NFE) AF: 0.202 AC: 13715 AN: 67994

Other (OTH) AF: 0.245 AC: 517 AN: 2112

Alfa AF: 0.206 Hom.: 10472

Bravo AF: 0.189

Asia WGS AF: 0.288 AC: 1000 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	0.46
DANN	Benign	0.67
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs10512934; hg19: chr5-7936287;