rs1837253

Variant names:

• chr5-111066174-T-C
• rs1837253

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 0.717 in 152,110 control chromosomes in the GnomAD database, including 39,434 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 0.72 (39434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 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: 0.717 AC: 108974 AN: 151992 Hom.: 39407 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.717 AC: 109055 AN: 152110 Hom.: 39434 Cov.: 32 AF XY: 0.713 AC XY: 53004 AN XY: 74354

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.720

Alfa AF: 0.730 Hom.: 83108

Bravo AF: 0.720

Asia WGS AF: 0.515 AC: 1793 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	2.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1837253; hg19: chr5-110401872;