chr5-36569651-G-T

Variant names:

• chr5-36569651-G-T
• rs7715271

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 0.369 in 151,946 control chromosomes in the GnomAD database, including 11,390 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 0.37 (11390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 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: 0.369 AC: 56038 AN: 151828 Hom.: 11366 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.369 AC: 56104 AN: 151946 Hom.: 11390 Cov.: 32 AF XY: 0.366 AC XY: 27163 AN XY: 74268

African (AFR) AF: 0.523 AC: 21622 AN: 41370

American (AMR) AF: 0.272 AC: 4156 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3468

East Asian (EAS) AF: 0.138 AC: 716 AN: 5172

South Asian (SAS) AF: 0.111 AC: 537 AN: 4822

European-Finnish (FIN) AF: 0.431 AC: 4545 AN: 10550

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22786 AN: 67966

Other (OTH) AF: 0.339 AC: 717 AN: 2116

Alfa AF: 0.331 Hom.: 4067

Bravo AF: 0.367

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.55
DANN	Benign	0.79
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs7715271; hg19: chr5-36569753;