rs4027875

Variant names:

• chr6-118401426-A-G
• rs4027875

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 0.641 in 152,042 control chromosomes in the GnomAD database, including 31,756 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 0.64 (31756 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 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: 0.641 AC: 97424 AN: 151924 Hom.: 31722 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.641 AC: 97506 AN: 152042 Hom.: 31756 Cov.: 32 AF XY: 0.637 AC XY: 47304 AN XY: 74304

African (AFR) AF: 0.687 AC: 28518 AN: 41484

American (AMR) AF: 0.496 AC: 7568 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2308 AN: 3470

East Asian (EAS) AF: 0.353 AC: 1822 AN: 5162

South Asian (SAS) AF: 0.642 AC: 3090 AN: 4816

European-Finnish (FIN) AF: 0.648 AC: 6845 AN: 10566

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45330 AN: 67958

Other (OTH) AF: 0.614 AC: 1298 AN: 2114

Alfa AF: 0.663 Hom.: 17355

Bravo AF: 0.626

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.33
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs4027875; hg19: chr6-118722589;