11-102538349-T-C

Variant names:

• chr11-102538349-T-C
• rs4754850

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.236 in 152,132 control chromosomes in the GnomAD database, including 4,381 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 0.24 (4381 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 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: 0.237 AC: 35963 AN: 152014 Hom.: 4379 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.236 AC: 35973 AN: 152132 Hom.: 4381 Cov.: 32 AF XY: 0.239 AC XY: 17787 AN XY: 74362

African (AFR) AF: 0.192 AC: 7960 AN: 41508

American (AMR) AF: 0.257 AC: 3920 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1411 AN: 5180

South Asian (SAS) AF: 0.235 AC: 1135 AN: 4828

European-Finnish (FIN) AF: 0.291 AC: 3073 AN: 10558

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16969 AN: 67992

Other (OTH) AF: 0.235 AC: 497 AN: 2112

Alfa AF: 0.241 Hom.: 3143

Bravo AF: 0.233

Asia WGS AF: 0.233 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.014
DANN	Benign	0.64
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4754850; hg19: chr11-102409080;