4-155013255-T-G

Variant names:

• chr4-155013255-T-G
• rs7684755
• ENST00000811698.1:n.115-5265A>C

Variant summary

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

The ENST00000811698.1(ENSG00000305561):​n.115-5265A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 151,852 control chromosomes in the GnomAD database, including 33,599 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 0.66 (33599 hom., cov: 31)
• Consequence: ENSG00000305561 ENST00000811698.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 1 publications found

Genes affected

ENSG00000305561 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811698.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305561	ENST00000811698.1		n.115-5265A>C		intron	N/A
	ENSG00000305561	ENST00000811699.1		n.78-2598A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100399 AN: 151734 Hom.: 33594 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.661 AC: 100435 AN: 151852 Hom.: 33599 Cov.: 31 AF XY: 0.659 AC XY: 48894 AN XY: 74210

African (AFR) AF: 0.572 AC: 23715 AN: 41438

American (AMR) AF: 0.661 AC: 10057 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2520 AN: 3466

East Asian (EAS) AF: 0.513 AC: 2643 AN: 5152

South Asian (SAS) AF: 0.648 AC: 3120 AN: 4818

European-Finnish (FIN) AF: 0.707 AC: 7432 AN: 10516

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48751 AN: 67938

Other (OTH) AF: 0.670 AC: 1412 AN: 2106

Alfa AF: 0.683 Hom.: 7222

Bravo AF: 0.656

Asia WGS AF: 0.602 AC: 2093 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.5
DANN	Benign	0.77
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7684755; hg19: chr4-155934407;