rs8037309

Variant names:

• chr15-37858237-C-T
• rs8037309
• ENST00000772735.1:n.388-16712G>A

Variant summary

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

The ENST00000772735.1(ENSG00000300563):​n.388-16712G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,026 control chromosomes in the GnomAD database, including 1,175 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 0.11 (1175 hom., cov: 32)
• Consequence: ENSG00000300563 ENST00000772735.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 3 publications found

Genes affected

ENSG00000300563 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 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
ENSG00000300563	ENST00000772735.1	n.388-16712G>A		intron_variant	Intron 3 of 4
ENSG00000300563	ENST00000772736.1	n.355-16712G>A		intron_variant	Intron 3 of 4
ENSG00000300563	ENST00000772737.1	n.425-16712G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16968 AN: 151906 Hom.: 1171 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.0935

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0517

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0729

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.112 AC: 17001 AN: 152026 Hom.: 1175 Cov.: 32 AF XY: 0.115 AC XY: 8569 AN XY: 74308

African (AFR) AF: 0.161 AC: 6683 AN: 41432

American (AMR) AF: 0.193 AC: 2954 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 214 AN: 3468

East Asian (EAS) AF: 0.0935 AC: 483 AN: 5166

South Asian (SAS) AF: 0.184 AC: 887 AN: 4824

European-Finnish (FIN) AF: 0.0517 AC: 546 AN: 10570

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0729 AC: 4955 AN: 67974

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.0876 Hom.: 1123

Bravo AF: 0.121

Asia WGS AF: 0.139 AC: 483 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	1.9
DANN	Benign	0.72
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs8037309; hg19: chr15-38150438;