rs743862

Variant names:

• chr6-32414162-T-C
• rs743862
• ENST00000766247.1:n.151-77T>C

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.151-77T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,068 control chromosomes in the GnomAD database, including 7,470 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 0.30 (7470 hom., cov: 31)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 18 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 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
ENSG00000299769	ENST00000766247.1	n.151-77T>C		intron_variant	Intron 1 of 2
ENSG00000299769	ENST00000766248.1	n.155-77T>C		intron_variant	Intron 1 of 3
ENSG00000299769	ENST00000766249.1	n.150-77T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46105 AN: 151950 Hom.: 7463 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0827

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.303 AC: 46134 AN: 152068 Hom.: 7470 Cov.: 31 AF XY: 0.299 AC XY: 22230 AN XY: 74314

African (AFR) AF: 0.306 AC: 12716 AN: 41498

American (AMR) AF: 0.239 AC: 3652 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3468

East Asian (EAS) AF: 0.0825 AC: 428 AN: 5188

South Asian (SAS) AF: 0.154 AC: 741 AN: 4816

European-Finnish (FIN) AF: 0.422 AC: 4450 AN: 10534

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.331 AC: 22522 AN: 67966

Other (OTH) AF: 0.282 AC: 594 AN: 2110

Alfa AF: 0.321 Hom.: 8289

Bravo AF: 0.290

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.47
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs743862; hg19: chr6-32381939;