8-127537878-A-G

Variant names:

• chr8-127537878-A-G
• rs4407842

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 0.587 in 152,148 control chromosomes in the GnomAD database, including 26,512 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 0.59 (26512 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 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: 0.587 AC: 89183 AN: 152028 Hom.: 26469 Cov.: 34

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.587 AC: 89281 AN: 152148 Hom.: 26512 Cov.: 34 AF XY: 0.590 AC XY: 43898 AN XY: 74388

African (AFR) AF: 0.652 AC: 27067 AN: 41502

American (AMR) AF: 0.584 AC: 8928 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1977 AN: 3470

East Asian (EAS) AF: 0.559 AC: 2888 AN: 5168

South Asian (SAS) AF: 0.610 AC: 2945 AN: 4828

European-Finnish (FIN) AF: 0.595 AC: 6301 AN: 10582

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37317 AN: 67978

Other (OTH) AF: 0.575 AC: 1217 AN: 2116

Alfa AF: 0.564 Hom.: 67876

Bravo AF: 0.587

Asia WGS AF: 0.613 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.64
PhyloP100		0.087

Splicing

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

Other links and lift over

dbSNP: rs4407842; hg19: chr8-128550123;