rs916598

chr7-127286837-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 0.574 in 152,200 control chromosomes in the GnomAD database, including 28,090 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 0.57 (28090 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87231 AN: 152080 Hom.: 28049 Cov.: 33

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.574 AC: 87311 AN: 152200 Hom.: 28090 Cov.: 33 AF XY: 0.561 AC XY: 41768 AN XY: 74408

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.579

Alfa AF: 0.506 Hom.: 41178

Bravo AF: 0.595

Asia WGS AF: 0.321 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.1
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs916598; hg19: chr7-126926891;