chr7-128239891-A-G

Position:

• chr7-128239891-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.397 in 151,886 control chromosomes in the GnomAD database, including 12,775 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 0.40 (12775 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60262 AN: 151770 Hom.: 12774 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.397 AC: 60294 AN: 151886 Hom.: 12775 Cov.: 32 AF XY: 0.392 AC XY: 29130 AN XY: 74252

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.434

Alfa AF: 0.373 Hom.: 2408

Bravo AF: 0.398

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13228377; hg19: chr7-127879944;