rs12197115

Variant names:

• chr6-69614241-C-T
• rs12197115
• ENST00000805732.1:n.108-11007G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000805732.1(ENSG00000304708):​n.108-11007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0229 in 152,252 control chromosomes in the GnomAD database, including 79 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 0.023 (79 hom., cov: 32)
• Consequence: ENSG00000304708 ENST00000805732.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 1 publications found

Genes affected

ENSG00000304708 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0229 (3481/152252) while in subpopulation AFR AF = 0.051 (2118/41530). AF 95% confidence interval is 0.0492. There are 79 homozygotes in GnomAd4. There are 1703 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 79 gene

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
ENSG00000304708	ENST00000805732.1	n.108-11007G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0228 AC: 3476 AN: 152134 Hom.: 79 Cov.: 32

Gnomad AFR AF: 0.0510

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0151

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.00518

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00929

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0229 AC: 3481 AN: 152252 Hom.: 79 Cov.: 32 AF XY: 0.0229 AC XY: 1703 AN XY: 74458

African (AFR) AF: 0.0510 AC: 2118 AN: 41530

American (AMR) AF: 0.0150 AC: 230 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3472

East Asian (EAS) AF: 0.0322 AC: 167 AN: 5190

South Asian (SAS) AF: 0.0268 AC: 129 AN: 4820

European-Finnish (FIN) AF: 0.00518 AC: 55 AN: 10608

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00929 AC: 632 AN: 68010

Other (OTH) AF: 0.0161 AC: 34 AN: 2114

Alfa AF: 0.0162 Hom.: 6

Bravo AF: 0.0250

Asia WGS AF: 0.0290 AC: 103 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	0.23
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12197115; hg19: chr6-70324133;