rs11142387

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;