5-95611429-G-T

Variant names:

• chr5-95611429-G-T
• rs956274

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 0.489 in 151,982 control chromosomes in the GnomAD database, including 20,499 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 0.49 (20499 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 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: 0.489 AC: 74191 AN: 151864 Hom.: 20448 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.489 AC: 74305 AN: 151982 Hom.: 20499 Cov.: 32 AF XY: 0.485 AC XY: 36056 AN XY: 74308

African (AFR) AF: 0.757 AC: 31376 AN: 41456

American (AMR) AF: 0.469 AC: 7154 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1545 AN: 3464

East Asian (EAS) AF: 0.510 AC: 2636 AN: 5172

South Asian (SAS) AF: 0.489 AC: 2353 AN: 4810

European-Finnish (FIN) AF: 0.286 AC: 3014 AN: 10542

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24835 AN: 67954

Other (OTH) AF: 0.477 AC: 1007 AN: 2112

Alfa AF: 0.429 Hom.: 12250

Bravo AF: 0.511

Asia WGS AF: 0.481 AC: 1672 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.24
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs956274; hg19: chr5-94947133; COSMIC: COSV60168081;