rs7177055

Variant names:

• chr15-77540420-G-A
• rs7177055
• ENST00000725805.1:n.212+23064G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000725805.1(ENSG00000259420):​n.212+23064G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000259420 ENST00000725805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 69 publications found

Genes affected

ENSG00000259420 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725805.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259420	ENST00000725805.1		n.212+23064G>A		intron	N/A
	ENSG00000259420	ENST00000725806.1		n.206+15739G>A		intron	N/A
	ENSG00000259420	ENST00000725808.1		n.114+4134G>A		intron	N/A

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

African (AFR) AF: 0.366 AC: 15163 AN: 41474

American (AMR) AF: 0.597 AC: 9118 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2436 AN: 3472

East Asian (EAS) AF: 0.355 AC: 1831 AN: 5162

South Asian (SAS) AF: 0.501 AC: 2416 AN: 4822

European-Finnish (FIN) AF: 0.675 AC: 7118 AN: 10552

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48478 AN: 67950

Other (OTH) AF: 0.602 AC: 1272 AN: 2114

Alfa AF: 0.669 Hom.: 160755

Bravo AF: 0.570

Asia WGS AF: 0.466 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.89
DANN	Benign	0.75
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs7177055; hg19: chr15-77832762;