4-177220482-T-C

Variant names:

• chr4-177220482-T-C
• rs1371231
• ENST00000763800.1:n.398A>G

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.301+5A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,738 control chromosomes in the GnomAD database, including 31,805 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 0.60 (31805 hom., cov: 33)
• Consequence: ENSG00000287544 ENST00000656694.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 5 publications found

Genes affected

ENSG00000287544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656694.1. 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
	ENSG00000287544	ENST00000763800.1		n.398A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000287544	ENST00000763801.1		n.835A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000287544	ENST00000763802.1		n.774A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.600 AC: 90922 AN: 151616 Hom.: 31798 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.599 AC: 90941 AN: 151738 Hom.: 31805 Cov.: 33 AF XY: 0.594 AC XY: 44031 AN XY: 74130

African (AFR) AF: 0.256 AC: 10624 AN: 41448

American (AMR) AF: 0.634 AC: 9647 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1126 AN: 5164

South Asian (SAS) AF: 0.639 AC: 3078 AN: 4818

European-Finnish (FIN) AF: 0.704 AC: 7380 AN: 10480

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54016 AN: 67838

Other (OTH) AF: 0.645 AC: 1359 AN: 2106

Alfa AF: 0.665 Hom.: 4606

Bravo AF: 0.581

Asia WGS AF: 0.432 AC: 1506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.38
PhyloP100		0.15

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: rs1371231;

hg19: chr4-178141636;