4-144498358-T-C

Variant names:

• chr4-144498358-T-C
• rs7684769
• ENST00000649263.1:n.328-82380A>G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-82380A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,056 control chromosomes in the GnomAD database, including 33,043 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 0.66 (33043 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427
• Publications: 3 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285713	ENST00000649263.1		n.328-82380A>G		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000648340.1		n.138+10883A>G		intron	N/A
	ENSG00000285783	ENST00000650526.1		n.223-82380A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99906 AN: 151938 Hom.: 33011 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.658 AC: 99981 AN: 152056 Hom.: 33043 Cov.: 32 AF XY: 0.658 AC XY: 48872 AN XY: 74292

African (AFR) AF: 0.615 AC: 25508 AN: 41462

American (AMR) AF: 0.595 AC: 9093 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2224 AN: 3470

East Asian (EAS) AF: 0.669 AC: 3446 AN: 5154

South Asian (SAS) AF: 0.663 AC: 3195 AN: 4818

European-Finnish (FIN) AF: 0.714 AC: 7557 AN: 10580

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46767 AN: 67990

Other (OTH) AF: 0.641 AC: 1351 AN: 2106

Alfa AF: 0.672 Hom.: 54868

Bravo AF: 0.645

Asia WGS AF: 0.583 AC: 2027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.14
DANN	Benign	0.76
PhyloP100		-0.43

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7684769;

hg19: chr4-145419510;