rs901540

Variant names:

• chr11-98980255-A-C
• rs901540

Your query was ambiguous. Multiple possible variants found:

• chr11-98980255-A-C
• chr11-98980255-A-G
• chr11-98980255-A-T

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 0.483 in 151,954 control chromosomes in the GnomAD database, including 19,543 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 0.48 (19543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.6 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: 0.483 AC: 73375 AN: 151836 Hom.: 19537 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.483 AC: 73396 AN: 151954 Hom.: 19543 Cov.: 32 AF XY: 0.488 AC XY: 36202 AN XY: 74246

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.481

Alfa AF: 0.556 Hom.: 35183

Bravo AF: 0.468

Asia WGS AF: 0.473 AC: 1641 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs901540; hg19: chr11-98850985;