rs704744

Variant names:

• chr11-34715014-A-G
• rs704744
• ENST00000843058.1:n.757A>G

Variant summary

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

The ENST00000843058.1(ENSG00000309692):​n.757A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,962 control chromosomes in the GnomAD database, including 20,597 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 0.51 (20597 hom., cov: 31)
• Consequence: ENSG00000309692 ENST00000843058.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807
• Publications: 2 publications found

Genes affected

ENSG00000309692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723568	XR_007062652.1	n.411-43A>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309692	ENST00000843058.1	n.757A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000309692	ENST00000843048.1	n.506+22125A>G		intron_variant	Intron 1 of 2
ENSG00000309692	ENST00000843049.1	n.698+12999A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77613 AN: 151842 Hom.: 20572 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.511 AC: 77677 AN: 151962 Hom.: 20597 Cov.: 31 AF XY: 0.502 AC XY: 37280 AN XY: 74258

African (AFR) AF: 0.570 AC: 23629 AN: 41432

American (AMR) AF: 0.384 AC: 5866 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1902 AN: 3470

East Asian (EAS) AF: 0.130 AC: 671 AN: 5166

South Asian (SAS) AF: 0.428 AC: 2061 AN: 4816

European-Finnish (FIN) AF: 0.466 AC: 4920 AN: 10550

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.540 AC: 36710 AN: 67950

Other (OTH) AF: 0.518 AC: 1094 AN: 2114

Alfa AF: 0.532 Hom.: 11215

Bravo AF: 0.503

Asia WGS AF: 0.245 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.57
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs704744; hg19: chr11-34736561;