4-71731104-G-T

Variant names:

• chr4-71731104-G-T
• rs6837549
• ENST00000726683.1:n.719-864G>T

Variant summary

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

The ENST00000726683.1(ENSG00000294912):​n.719-864G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,834 control chromosomes in the GnomAD database, including 17,169 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 0.47 (17169 hom., cov: 31)
• Consequence: ENSG00000294912 ENST00000726683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 7 publications found

Genes affected

ENSG00000294912 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726683.1. 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
	ENSG00000294912	ENST00000726683.1		n.719-864G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71222 AN: 151716 Hom.: 17172 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.469 AC: 71242 AN: 151834 Hom.: 17169 Cov.: 31 AF XY: 0.473 AC XY: 35061 AN XY: 74172

African (AFR) AF: 0.388 AC: 16070 AN: 41388

American (AMR) AF: 0.522 AC: 7965 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2071 AN: 3466

East Asian (EAS) AF: 0.273 AC: 1402 AN: 5134

South Asian (SAS) AF: 0.540 AC: 2606 AN: 4824

European-Finnish (FIN) AF: 0.546 AC: 5739 AN: 10506

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33736 AN: 67940

Other (OTH) AF: 0.476 AC: 1004 AN: 2110

Alfa AF: 0.487 Hom.: 56012

Bravo AF: 0.461

Asia WGS AF: 0.397 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs6837549; hg19: chr4-72596821;