9-70383416-A-C

Variant names:

• chr9-70383416-A-C
• rs11142387

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.374 AC: 15519 AN: 41440

American (AMR) AF: 0.515 AC: 7867 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1740 AN: 3468

East Asian (EAS) AF: 0.365 AC: 1882 AN: 5154

South Asian (SAS) AF: 0.666 AC: 3200 AN: 4802

European-Finnish (FIN) AF: 0.494 AC: 5224 AN: 10570

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.544 AC: 36960 AN: 67914

Other (OTH) AF: 0.495 AC: 1044 AN: 2110

Alfa AF: 0.521 Hom.: 64960

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs11142387; hg19: chr9-72998332;