rs11142387

Variant names:

• chr9-70383416-A-C
• rs11142387

Your query was ambiguous. Multiple possible variants found:

• chr9-70383416-A-C
• chr9-70383416-A-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 0.488 in 151,926 control chromosomes in the GnomAD database, including 18,664 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 0.49 (18664 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.647 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: 0.488 AC: 74130 AN: 151808 Hom.: 18642 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.488 AC: 74197 AN: 151926 Hom.: 18664 Cov.: 31 AF XY: 0.488 AC XY: 36228 AN XY: 74248

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.495

Alfa AF: 0.532 Hom.: 39511

Bravo AF: 0.480

Asia WGS AF: 0.533 AC: 1855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11142387; hg19: chr9-72998332;