rs749316

Positions:

• chr4-144450194-A-G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-34216T>C 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 151,932 control chromosomes in the GnomAD database, including 4,361 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 (4361 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.239-34216T>C		intron_variant
LOC105377462	XR_939273.3	n.165-34216T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-34216T>C		intron_variant				ENSP00000497507.1
ENSG00000285783	ENST00000648340.1	n.139-34216T>C		intron_variant
ENSG00000285783	ENST00000650526.1	n.223-34216T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34573 AN: 151814 Hom.: 4364 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.228 AC: 34584 AN: 151932 Hom.: 4361 Cov.: 31 AF XY: 0.225 AC XY: 16697 AN XY: 74248

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.245

Alfa AF: 0.266 Hom.: 6514

Bravo AF: 0.232

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs749316; hg19: chr4-145371346;