5-126846170-T-C

Variant names:

• chr5-126846170-T-C
• rs959573

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 0.712 in 152,136 control chromosomes in the GnomAD database, including 38,836 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 0.71 (38836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 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: 0.712 AC: 108237 AN: 152018 Hom.: 38802 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.712 AC: 108326 AN: 152136 Hom.: 38836 Cov.: 32 AF XY: 0.718 AC XY: 53365 AN XY: 74372

African (AFR) AF: 0.756 AC: 31377 AN: 41494

American (AMR) AF: 0.701 AC: 10722 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2346 AN: 3472

East Asian (EAS) AF: 0.629 AC: 3254 AN: 5176

South Asian (SAS) AF: 0.643 AC: 3093 AN: 4814

European-Finnish (FIN) AF: 0.801 AC: 8474 AN: 10574

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46761 AN: 67996

Other (OTH) AF: 0.690 AC: 1454 AN: 2108

Alfa AF: 0.694 Hom.: 159361

Bravo AF: 0.707

Asia WGS AF: 0.641 AC: 2229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.35
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs959573; hg19: chr5-126181862;