rs7177055

Positions:

• chr15-77540420-G-A

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 0.583 in 152,030 control chromosomes in the GnomAD database, including 27,721 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 0.58 (27721 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 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: 0.583 AC: 88621 AN: 151912 Hom.: 27695 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.583 AC: 88690 AN: 152030 Hom.: 27721 Cov.: 32 AF XY: 0.577 AC XY: 42853 AN XY: 74280

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.602

Alfa AF: 0.680 Hom.: 83564

Bravo AF: 0.570

Asia WGS AF: 0.466 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.89
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7177055; hg19: chr15-77832762;