4-188951696-T-C

Variant names:

• chr4-188951696-T-C
• rs10004892
• ENST00000746829.1:n.110+8714T>C

Variant summary

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

The ENST00000746829.1(ENSG00000297289):​n.110+8714T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,066 control chromosomes in the GnomAD database, including 3,464 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 0.21 (3464 hom., cov: 33)
• Consequence: ENSG00000297289 ENST00000746829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 3 publications found

Genes affected

ENSG00000297289 (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 (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746829.1. 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
	ENSG00000297289	ENST00000746829.1		n.110+8714T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31644 AN: 151946 Hom.: 3467 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.208 AC: 31653 AN: 152066 Hom.: 3464 Cov.: 33 AF XY: 0.206 AC XY: 15331 AN XY: 74336

African (AFR) AF: 0.170 AC: 7034 AN: 41498

American (AMR) AF: 0.157 AC: 2396 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3470

East Asian (EAS) AF: 0.165 AC: 851 AN: 5168

South Asian (SAS) AF: 0.206 AC: 992 AN: 4824

European-Finnish (FIN) AF: 0.235 AC: 2485 AN: 10568

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16699 AN: 67944

Other (OTH) AF: 0.193 AC: 407 AN: 2112

Alfa AF: 0.223 Hom.: 800

Bravo AF: 0.199

Asia WGS AF: 0.183 AC: 636 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.59
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10004892; hg19: chr4-189872850;