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

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

Gnomad4 AFR AF: 0.881 AC: 0.881355 AN: 0.881355

Gnomad4 AMR AF: 0.573 AC: 0.573206 AN: 0.573206

Gnomad4 ASJ AF: 0.652 AC: 0.651585 AN: 0.651585

Gnomad4 EAS AF: 0.676 AC: 0.67589 AN: 0.67589

Gnomad4 SAS AF: 0.767 AC: 0.767331 AN: 0.767331

Gnomad4 FIN AF: 0.668 AC: 0.668339 AN: 0.668339

Gnomad4 NFE AF: 0.661 AC: 0.661406 AN: 0.661406

Gnomad4 OTH AF: 0.670 AC: 0.669981 AN: 0.669981

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

Splicing

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

Publications

LitVar

Other links and lift over

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