rs11100040

Variant names:

• chr4-156085802-T-C
• rs11100040

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 0.642 in 150,536 control chromosomes in the GnomAD database, including 33,658 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 0.64 (33658 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.781 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: 0.642 AC: 96574 AN: 150436 Hom.: 33647 Cov.: 26

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.642 AC: 96613 AN: 150536 Hom.: 33658 Cov.: 26 AF XY: 0.640 AC XY: 46931 AN XY: 73320

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.670

Alfa AF: 0.764 Hom.: 88298

Bravo AF: 0.625

Asia WGS AF: 0.661 AC: 2300 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.10
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11100040; hg19: chr4-157006954;