rs4757610

Positions:

• chr11-18047874-G-A

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 0.433 in 151,962 control chromosomes in the GnomAD database, including 14,796 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 0.43 (14796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.66

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 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: 0.433 AC: 65718 AN: 151844 Hom.: 14781 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.433 AC: 65784 AN: 151962 Hom.: 14796 Cov.: 32 AF XY: 0.425 AC XY: 31574 AN XY: 74274

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.436

Alfa AF: 0.421 Hom.: 1727

Bravo AF: 0.436

Asia WGS AF: 0.306 AC: 1069 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4757610; hg19: chr11-18069421;