chr4-177220387-T-G

Variant names:

• chr4-177220387-T-G
• rs1821970
• ENST00000656694.1:n.301+100A>C

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.301+100A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,278 control chromosomes in the GnomAD database, including 1,293 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 0.11 (1293 hom., cov: 33)
• Consequence: ENSG00000287544 ENST00000656694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 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	ENST00000656694.1		n.301+100A>C		intron	N/A
	ENSG00000287544	ENST00000662794.1		n.374+100A>C		intron	N/A
	ENSG00000287544	ENST00000667713.1		n.396+100A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17278 AN: 152160 Hom.: 1296 Cov.: 33

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0782

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.113 AC: 17266 AN: 152278 Hom.: 1293 Cov.: 33 AF XY: 0.117 AC XY: 8697 AN XY: 74460

African (AFR) AF: 0.0734 AC: 3050 AN: 41560

American (AMR) AF: 0.0783 AC: 1198 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2011 AN: 5172

South Asian (SAS) AF: 0.152 AC: 733 AN: 4828

European-Finnish (FIN) AF: 0.157 AC: 1667 AN: 10614

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7970 AN: 68024

Other (OTH) AF: 0.102 AC: 214 AN: 2108

Alfa AF: 0.109 Hom.: 119

Bravo AF: 0.105

Asia WGS AF: 0.256 AC: 888 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.88
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1821970; hg19: chr4-178141541;