rs6745746

Variant names:

• chr2-112852467-G-A
• rs6745746
• ENST00000762706.1:n.405-32791G>A

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.405-32791G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,888 control chromosomes in the GnomAD database, including 12,199 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 0.39 (12199 hom., cov: 31)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 5 publications found

Genes affected

ENSG00000299339 (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 (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762706.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299339	ENST00000762706.1		n.405-32791G>A		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.500-32791G>A		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.266-32791G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59728 AN: 151768 Hom.: 12205 Cov.: 31

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.393 AC: 59722 AN: 151888 Hom.: 12199 Cov.: 31 AF XY: 0.390 AC XY: 28947 AN XY: 74204

African (AFR) AF: 0.299 AC: 12365 AN: 41398

American (AMR) AF: 0.353 AC: 5395 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1475 AN: 3468

East Asian (EAS) AF: 0.473 AC: 2438 AN: 5158

South Asian (SAS) AF: 0.276 AC: 1331 AN: 4814

European-Finnish (FIN) AF: 0.391 AC: 4116 AN: 10526

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31272 AN: 67938

Other (OTH) AF: 0.393 AC: 830 AN: 2110

Alfa AF: 0.421 Hom.: 1726

Bravo AF: 0.391

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.49
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6745746; hg19: chr2-113610044;