rs7177316

Variant names:

• chr15-50129633-A-G
• rs7177316
• ENST00000895127.1:c.-42-22625T>C

Your query was ambiguous. Multiple possible variants found:

• chr15-50129633-A-G
• chr15-50129633-A-T

Variant summary

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

The ENST00000558829.1(ATP8B4):​c.-42-22625T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,026 control chromosomes in the GnomAD database, including 21,094 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 0.51 (21094 hom., cov: 31)
• Consequence: ATP8B4 ENST00000558829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 6 publications found

Genes affected

ATP8B4 (HGNC:13536): (ATPase phospholipid transporting 8B4 (putative)) This gene encodes a member of the cation transport ATPase (P-type) family and type IV subfamily. The encoded protein is involved in phospholipid transport in the cell membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558829.1. 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
	ATP8B4	ENST00000895127.1		c.-42-22625T>C		intron	N/A	ENSP00000565186.1
	ATP8B4	ENST00000966552.1		c.-42-22625T>C		intron	N/A	ENSP00000636611.1
	ATP8B4	ENST00000558829.1	TSL:3	c.-42-22625T>C		intron	N/A	ENSP00000453539.1	H0YMB5

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76921 AN: 151908 Hom.: 21087 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.506 AC: 76951 AN: 152026 Hom.: 21094 Cov.: 31 AF XY: 0.508 AC XY: 37720 AN XY: 74300

African (AFR) AF: 0.293 AC: 12159 AN: 41464

American (AMR) AF: 0.483 AC: 7377 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2299 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2344 AN: 5166

South Asian (SAS) AF: 0.485 AC: 2338 AN: 4822

European-Finnish (FIN) AF: 0.662 AC: 6995 AN: 10562

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41663 AN: 67952

Other (OTH) AF: 0.521 AC: 1098 AN: 2108

Alfa AF: 0.573 Hom.: 81089

Bravo AF: 0.479

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7177316;

hg19: chr15-50421830;