rs12110693

Variant names:

• chr6-121837124-G-A
• rs12110693
• ENST00000780084.1:n.193-20787G>A

Variant summary

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

The ENST00000780084.1(ENSG00000289871):​n.193-20787G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,004 control chromosomes in the GnomAD database, including 6,455 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 0.23 (6455 hom., cov: 32)
• Consequence: ENSG00000289871 ENST00000780084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 19 publications found

Genes affected

ENSG00000289871 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377979	XR_942936.3	n.238-20787G>A		intron_variant	Intron 1 of 6
LOC105377979	XR_942937.4	n.237+69509G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289871	ENST00000780084.1	n.193-20787G>A		intron_variant	Intron 1 of 4
ENSG00000289871	ENST00000780085.1	n.80-20787G>A		intron_variant	Intron 1 of 3
ENSG00000289871	ENST00000780086.1	n.109-28729G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34438 AN: 151886 Hom.: 6421 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0998

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.227 AC: 34519 AN: 152004 Hom.: 6455 Cov.: 32 AF XY: 0.226 AC XY: 16794 AN XY: 74284

African (AFR) AF: 0.502 AC: 20788 AN: 41432

American (AMR) AF: 0.123 AC: 1872 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0980 AC: 340 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2340 AN: 5146

South Asian (SAS) AF: 0.106 AC: 511 AN: 4818

European-Finnish (FIN) AF: 0.132 AC: 1392 AN: 10574

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.0998 AC: 6784 AN: 67980

Other (OTH) AF: 0.203 AC: 429 AN: 2110

Alfa AF: 0.151 Hom.: 7205

Bravo AF: 0.240

Asia WGS AF: 0.306 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.60
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs12110693; hg19: chr6-122158270;