rs6747506

Variant names:

• chr2-73294754-A-T
• rs6747506
• ENST00000846694.1:n.174-3812A>T

Variant summary

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

The ENST00000846694.1(ENSG00000310032):​n.174-3812A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,780 control chromosomes in the GnomAD database, including 7,873 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 0.23 (7873 hom., cov: 32)
• Consequence: ENSG00000310032 ENST00000846694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 4 publications found

Genes affected

ENSG00000310032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 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
ENSG00000310032	ENST00000846694.1	n.174-3812A>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35536 AN: 151662 Hom.: 7835 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0562

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.235 AC: 35637 AN: 151780 Hom.: 7873 Cov.: 32 AF XY: 0.235 AC XY: 17464 AN XY: 74188

African (AFR) AF: 0.569 AC: 23454 AN: 41252

American (AMR) AF: 0.210 AC: 3205 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3472

East Asian (EAS) AF: 0.423 AC: 2180 AN: 5152

South Asian (SAS) AF: 0.222 AC: 1064 AN: 4798

European-Finnish (FIN) AF: 0.0562 AC: 593 AN: 10552

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.0610 AC: 4145 AN: 67988

Other (OTH) AF: 0.206 AC: 434 AN: 2108

Alfa AF: 0.157 Hom.: 613

Bravo AF: 0.265

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.0
DANN	Benign	0.86
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs6747506; hg19: chr2-73521882;