rs7744666

Variant names:

• chr6-32891935-T-C
• rs7744666
• ENST00000753352.1:n.858A>G

Variant summary

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

The ENST00000753352.1(ENSG00000289559):​n.858A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,168 control chromosomes in the GnomAD database, including 1,462 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 0.13 (1462 hom., cov: 32)
• Consequence: ENSG00000289559 ENST00000753352.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 8 publications found

Genes affected

ENSG00000289559 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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
ENSG00000289559	ENST00000753352.1	n.858A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000289559	ENST00000753353.1	n.509A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000289559	ENST00000753354.1	n.417A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19609 AN: 152050 Hom.: 1456 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0953

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.129 AC: 19653 AN: 152168 Hom.: 1462 Cov.: 32 AF XY: 0.130 AC XY: 9645 AN XY: 74408

African (AFR) AF: 0.193 AC: 8023 AN: 41488

American (AMR) AF: 0.0952 AC: 1457 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3470

East Asian (EAS) AF: 0.0869 AC: 451 AN: 5188

South Asian (SAS) AF: 0.141 AC: 680 AN: 4820

European-Finnish (FIN) AF: 0.114 AC: 1204 AN: 10592

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6839 AN: 67994

Other (OTH) AF: 0.121 AC: 255 AN: 2110

Alfa AF: 0.119 Hom.: 160

Bravo AF: 0.128

Asia WGS AF: 0.141 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.44
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs7744666; hg19: chr6-32859712;