rs4938174

Variant names:

• chr11-111042516-G-A
• rs4938174

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 0.309 in 151,994 control chromosomes in the GnomAD database, including 7,453 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 0.31 (7453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719

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 (AFR) allele frequency at 95% confidence interval = 0.375 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: 0.309 AC: 46940 AN: 151876 Hom.: 7449 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0960

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.309 AC: 46956 AN: 151994 Hom.: 7453 Cov.: 32 AF XY: 0.307 AC XY: 22773 AN XY: 74284

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.0963

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.320

Alfa AF: 0.299 Hom.: 14193

Bravo AF: 0.308

Asia WGS AF: 0.156 AC: 544 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	8.3
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4938174; hg19: chr11-110913240;