chr4-148713873-C-T

Position:

• chr4-148713873-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661928.1(ENSG00000287292):​n.223-152884C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,934 control chromosomes in the GnomAD database, including 4,007 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 0.22 (4007 hom., cov: 32)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523

Genes affected

ENSG00000287292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986195	XR_001741441.2	n.3662-152884C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287292	ENST00000661928.1	n.223-152884C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32855 AN: 151818 Hom.: 4008 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0622

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.216 AC: 32873 AN: 151934 Hom.: 4007 Cov.: 32 AF XY: 0.210 AC XY: 15579 AN XY: 74236

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0621

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.216

Alfa AF: 0.194 Hom.: 6383

Bravo AF: 0.228

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519980; hg19: chr4-149635025;