4-144570851-T-C

Variant names:

• chr4-144570851-T-C
• rs6817273
• ENST00000649263.1:n.328-154873A>G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-154873A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,754 control chromosomes in the GnomAD database, including 10,031 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 0.34 (10031 hom., cov: 30)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 13 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-154873A>G		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-154873A>G		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51220 AN: 151638 Hom.: 10023 Cov.: 30

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.338 AC: 51250 AN: 151754 Hom.: 10031 Cov.: 30 AF XY: 0.345 AC XY: 25538 AN XY: 74128

African (AFR) AF: 0.144 AC: 5949 AN: 41422

American (AMR) AF: 0.317 AC: 4830 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3464

East Asian (EAS) AF: 0.301 AC: 1543 AN: 5124

South Asian (SAS) AF: 0.519 AC: 2495 AN: 4808

European-Finnish (FIN) AF: 0.539 AC: 5652 AN: 10490

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.419 AC: 28435 AN: 67882

Other (OTH) AF: 0.321 AC: 675 AN: 2106

Alfa AF: 0.406 Hom.: 8020

Bravo AF: 0.305

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.50
DANN	Benign	0.81
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs6817273; hg19: chr4-145492003;