rs1837253

chr5-111066174-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 0.717 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;