rs719756

Variant names:

• chr5-42725527-T-A
• rs719756

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 0.454 in 152,030 control chromosomes in the GnomAD database, including 15,874 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 0.45 (15874 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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: 0.454 AC: 69043 AN: 151912 Hom.: 15881 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.454 AC: 69056 AN: 152030 Hom.: 15874 Cov.: 32 AF XY: 0.454 AC XY: 33746 AN XY: 74294

African (AFR) AF: 0.467 AC: 19363 AN: 41468

American (AMR) AF: 0.406 AC: 6202 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1549 AN: 3470

East Asian (EAS) AF: 0.582 AC: 3008 AN: 5166

South Asian (SAS) AF: 0.480 AC: 2310 AN: 4814

European-Finnish (FIN) AF: 0.370 AC: 3911 AN: 10564

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31245 AN: 67958

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.452 Hom.: 1930

Bravo AF: 0.458

Asia WGS AF: 0.544 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.74
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs719756; hg19: chr5-42725629;