rs7177055

Variant names:

• chr15-77540420-G-A
• rs7177055

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;