rs397703

Variant names:

• chr13-33013191-T-C
• rs397703
• ENST00000830674.1:n.854A>G

Variant summary

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

The ENST00000830674.1(ENSG00000308044):​n.854A>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 0.172 in 152,172 control chromosomes in the GnomAD database, including 2,377 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 0.17 (2377 hom., cov: 32)
• Consequence: ENSG00000308044 ENST00000830674.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 7 publications found

Genes affected

ENSG00000308044 (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 (AMR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903151	XR_007063749.1	n.662A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124903151	XM_047430819.1	c.*254A>G		3_prime_UTR_variant	Exon 2 of 2		XP_047286775.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308044	ENST00000830674.1	n.854A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308044	ENST00000830675.1	n.1017A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308044	ENST00000830677.1	n.589A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308044	ENST00000830676.1	n.*174A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26115 AN: 152054 Hom.: 2373 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.172 AC: 26124 AN: 152172 Hom.: 2377 Cov.: 32 AF XY: 0.173 AC XY: 12901 AN XY: 74388

African (AFR) AF: 0.104 AC: 4330 AN: 41532

American (AMR) AF: 0.219 AC: 3357 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3472

East Asian (EAS) AF: 0.138 AC: 716 AN: 5170

South Asian (SAS) AF: 0.167 AC: 805 AN: 4820

European-Finnish (FIN) AF: 0.221 AC: 2334 AN: 10564

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13463 AN: 67998

Other (OTH) AF: 0.163 AC: 344 AN: 2110

Alfa AF: 0.186 Hom.: 1284

Bravo AF: 0.170

Asia WGS AF: 0.158 AC: 550 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	4.2
DANN	Benign	0.37
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs397703; hg19: chr13-33587329;