4-144305270-G-A

Variant names:

• chr4-144305270-G-A
• rs11935505
• ENST00000649263.1:n.*44-22084C>T

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.*44-22084C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,012 control chromosomes in the GnomAD database, including 2,489 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 0.14 (2489 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765
• Publications: 1 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=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. 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
	ENSG00000285713	ENST00000649263.1		n.*44-22084C>T		intron	N/A	ENSP00000497507.1
	ENSG00000285783	ENST00000648340.1		n.215-22084C>T		intron	N/A
	ENSG00000285783	ENST00000650526.1		n.299-22084C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21291 AN: 151894 Hom.: 2483 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0447

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0534

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.140 AC: 21332 AN: 152012 Hom.: 2489 Cov.: 32 AF XY: 0.138 AC XY: 10270 AN XY: 74308

African (AFR) AF: 0.328 AC: 13599 AN: 41414

American (AMR) AF: 0.135 AC: 2061 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3470

East Asian (EAS) AF: 0.146 AC: 755 AN: 5170

South Asian (SAS) AF: 0.0387 AC: 187 AN: 4826

European-Finnish (FIN) AF: 0.0447 AC: 474 AN: 10594

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0534 AC: 3632 AN: 67964

Other (OTH) AF: 0.130 AC: 274 AN: 2110

Alfa AF: 0.0720 Hom.: 1003

Bravo AF: 0.157

Asia WGS AF: 0.110 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs11935505; hg19: chr4-145226422;