4-144510345-A-G

Variant names:

• chr4-144510345-A-G
• rs1512282
• ENST00000649263.1:n.328-94367T>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-94367T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,064 control chromosomes in the GnomAD database, including 9,272 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 0.33 (9272 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 14 publications found

Genes affected

ENSG00000285713 (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 (SAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.165-10825T>C		intron_variant	Intron 1 of 7
LOC105377462	XR_939273.3	n.164+51639T>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-94367T>C		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-94367T>C		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50262 AN: 151946 Hom.: 9265 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.331 AC: 50278 AN: 152064 Hom.: 9272 Cov.: 32 AF XY: 0.337 AC XY: 25046 AN XY: 74318

African (AFR) AF: 0.168 AC: 6980 AN: 41508

American (AMR) AF: 0.314 AC: 4789 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1130 AN: 3466

East Asian (EAS) AF: 0.308 AC: 1582 AN: 5138

South Asian (SAS) AF: 0.530 AC: 2557 AN: 4824

European-Finnish (FIN) AF: 0.500 AC: 5289 AN: 10572

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26781 AN: 67968

Other (OTH) AF: 0.326 AC: 688 AN: 2112

Alfa AF: 0.375 Hom.: 47001

Bravo AF: 0.302

Asia WGS AF: 0.374 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.023
DANN	Benign	0.55
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1512282; hg19: chr4-145431497;