rs7716011

Variant names:

• chr5-158098845-T-G
• rs7716011

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 0.2 in 152,200 control chromosomes in the GnomAD database, including 3,308 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 0.20 (3308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 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: 0.200 AC: 30476 AN: 152080 Hom.: 3304 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.200 AC: 30493 AN: 152200 Hom.: 3308 Cov.: 32 AF XY: 0.199 AC XY: 14782 AN XY: 74414

African (AFR) AF: 0.122 AC: 5074 AN: 41506

American (AMR) AF: 0.244 AC: 3738 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3470

East Asian (EAS) AF: 0.0862 AC: 447 AN: 5184

South Asian (SAS) AF: 0.216 AC: 1043 AN: 4828

European-Finnish (FIN) AF: 0.200 AC: 2121 AN: 10600

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16763 AN: 68004

Other (OTH) AF: 0.197 AC: 416 AN: 2112

Alfa AF: 0.230 Hom.: 7463

Bravo AF: 0.198

Asia WGS AF: 0.166 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7716011; hg19: chr5-157525853;