rs3910198

Positions:

• chr5-127688390-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.619 in 151,866 control chromosomes in the GnomAD database, including 29,685 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 0.62 (29685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93967 AN: 151750 Hom.: 29643 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.619 AC: 94049 AN: 151866 Hom.: 29685 Cov.: 31 AF XY: 0.613 AC XY: 45490 AN XY: 74216

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.595

Alfa AF: 0.621 Hom.: 4181

Bravo AF: 0.604

Asia WGS AF: 0.405 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3910198; hg19: chr5-127024082;