rs9295740

Variant names:

• chr6-27721723-G-A
• rs9295740
• ENST00000783576.1:n.356-720C>T

Variant summary

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

The ENST00000783576.1(ENSG00000302043):​n.356-720C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,962 control chromosomes in the GnomAD database, including 6,355 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 0.26 (6355 hom., cov: 31)
• Consequence: ENSG00000302043 ENST00000783576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486
• Publications: 33 publications found

Genes affected

ENSG00000302043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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
ENSG00000302043	ENST00000783576.1	n.356-720C>T		intron_variant	Intron 2 of 4
ENSG00000302043	ENST00000783577.1	n.204-10827C>T		intron_variant	Intron 1 of 2
ENSG00000302043	ENST00000783578.1	n.302-10827C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39606 AN: 151844 Hom.: 6340 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.261 AC: 39664 AN: 151962 Hom.: 6355 Cov.: 31 AF XY: 0.256 AC XY: 19010 AN XY: 74292

African (AFR) AF: 0.457 AC: 18906 AN: 41400

American (AMR) AF: 0.241 AC: 3679 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3472

East Asian (EAS) AF: 0.187 AC: 967 AN: 5168

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4814

European-Finnish (FIN) AF: 0.120 AC: 1268 AN: 10582

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

European-Non Finnish (NFE) AF: 0.180 AC: 12241 AN: 67948

Other (OTH) AF: 0.252 AC: 531 AN: 2108

Alfa AF: 0.211 Hom.: 13379

Bravo AF: 0.278

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.9
DANN	Benign	0.80
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs9295740; hg19: chr6-27689502;