chr6-426155-G-C

Variant names:

• chr6-426155-G-C
• rs9378815

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 0.516 in 152,182 control chromosomes in the GnomAD database, including 22,071 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 0.52 (22071 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 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: 0.516 AC: 78513 AN: 152062 Hom.: 22067 Cov.: 34

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.516 AC: 78552 AN: 152182 Hom.: 22071 Cov.: 34 AF XY: 0.513 AC XY: 38182 AN XY: 74410

African (AFR) AF: 0.294 AC: 12185 AN: 41504

American (AMR) AF: 0.563 AC: 8616 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2391 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1785 AN: 5184

South Asian (SAS) AF: 0.474 AC: 2289 AN: 4826

European-Finnish (FIN) AF: 0.589 AC: 6242 AN: 10602

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43085 AN: 67984

Other (OTH) AF: 0.555 AC: 1169 AN: 2108

Alfa AF: 0.409 Hom.: 917

Bravo AF: 0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.20
DANN	Benign	0.19
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9378815; hg19: chr6-426155;