chr8-127776739-A-G

Variant names:

• chr8-127776739-A-G
• rs4395860

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 0.717 in 152,094 control chromosomes in the GnomAD database, including 39,999 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 0.72 (39999 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 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: 0.716 AC: 108880 AN: 151976 Hom.: 39942 Cov.: 32

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.717 AC: 108995 AN: 152094 Hom.: 39999 Cov.: 32 AF XY: 0.715 AC XY: 53171 AN XY: 74340

African (AFR) AF: 0.881 AC: 36578 AN: 41502

American (AMR) AF: 0.573 AC: 8754 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2261 AN: 3470

East Asian (EAS) AF: 0.676 AC: 3493 AN: 5168

South Asian (SAS) AF: 0.767 AC: 3697 AN: 4818

European-Finnish (FIN) AF: 0.668 AC: 7059 AN: 10562

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44965 AN: 67984

Other (OTH) AF: 0.670 AC: 1415 AN: 2112

Alfa AF: 0.675 Hom.: 32993

Bravo AF: 0.714

Asia WGS AF: 0.752 AC: 2619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs4395860; hg19: chr8-128788985; COSMIC: COSV104527703;