rs4757610

Variant names:

• chr11-18047874-G-A
• rs4757610

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;