chr4-182889660-C-T

Variant names:

• chr4-182889660-C-T
• rs6834938
• ENST00000795667.1:n.164-3937C>T

Variant summary

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

The ENST00000795667.1(ENSG00000303565):​n.164-3937C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,270 control chromosomes in the GnomAD database, including 4,658 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 0.23 (4658 hom., cov: 33)
• Consequence: ENSG00000303565 ENST00000795667.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 5 publications found

Genes affected

ENSG00000303565 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795667.1. 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
	ENSG00000303565	ENST00000795667.1		n.164-3937C>T		intron	N/A
	ENSG00000303565	ENST00000795668.1		n.305-3940C>T		intron	N/A
	ENSG00000303565	ENST00000795669.1		n.349-3940C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34473 AN: 151152 Hom.: 4658 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.228 AC: 34498 AN: 151270 Hom.: 4658 Cov.: 33 AF XY: 0.230 AC XY: 17013 AN XY: 73946

African (AFR) AF: 0.367 AC: 14929 AN: 40650

American (AMR) AF: 0.244 AC: 3718 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3466

East Asian (EAS) AF: 0.264 AC: 1365 AN: 5166

South Asian (SAS) AF: 0.253 AC: 1221 AN: 4826

European-Finnish (FIN) AF: 0.161 AC: 1699 AN: 10578

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10420 AN: 68014

Other (OTH) AF: 0.221 AC: 466 AN: 2106

Alfa AF: 0.176 Hom.: 4418

Bravo AF: 0.239

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.85
PhyloP100		-2.2

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: rs6834938;

hg19: chr4-183810813;