rs4378061

Variant names:

• chr9-10940127-C-T
• rs4378061

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 0.532 in 152,046 control chromosomes in the GnomAD database, including 23,668 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 0.53 (23668 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 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: 0.532 AC: 80783 AN: 151928 Hom.: 23638 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.532 AC: 80857 AN: 152046 Hom.: 23668 Cov.: 32 AF XY: 0.521 AC XY: 38724 AN XY: 74322

African (AFR) AF: 0.773 AC: 32085 AN: 41492

American (AMR) AF: 0.369 AC: 5642 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1890 AN: 3472

East Asian (EAS) AF: 0.107 AC: 550 AN: 5162

South Asian (SAS) AF: 0.327 AC: 1576 AN: 4818

European-Finnish (FIN) AF: 0.427 AC: 4509 AN: 10558

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32862 AN: 67962

Other (OTH) AF: 0.508 AC: 1070 AN: 2108

Alfa AF: 0.500 Hom.: 25904

Bravo AF: 0.538

Asia WGS AF: 0.262 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.0
DANN	Benign	0.35
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs4378061; hg19: chr9-10940127;