rs11239930

Variant names:

• chr1-147089017-G-A
• rs11239930

Your query was ambiguous. Multiple possible variants found:

• chr1-147089017-G-A
• chr1-147089017-G-T

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 0.473 in 151,896 control chromosomes in the GnomAD database, including 17,179 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 0.47 (17179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.62 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: 0.473 AC: 71803 AN: 151776 Hom.: 17156 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.473 AC: 71871 AN: 151896 Hom.: 17179 Cov.: 32 AF XY: 0.475 AC XY: 35286 AN XY: 74248

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.449

Alfa AF: 0.438 Hom.: 20449

Bravo AF: 0.478

Asia WGS AF: 0.572 AC: 1989 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11239930; hg19: chr1-146560564;