rs12189640

Variant names:

• chr6-27506878-T-C
• rs12189640
• ENST00000648816.1:n.107-10779A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000648816.1(ENSG00000285703):​n.107-10779A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 152,278 control chromosomes in the GnomAD database, including 264 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 0.049 (264 hom., cov: 32)
• Consequence: ENSG00000285703 ENST00000648816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

Genes affected

ENSG00000285703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0713 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
ENSG00000285703	ENST00000648816.1	n.107-10779A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7432 AN: 152162 Hom.: 264 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0328

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0212

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0730

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0488 AC: 7432 AN: 152278 Hom.: 264 Cov.: 32 AF XY: 0.0492 AC XY: 3661 AN XY: 74456

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.0328

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.0214

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0730

Gnomad4 OTH AF: 0.0345

Alfa AF: 0.0637 Hom.: 481

Bravo AF: 0.0430

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	16
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12189640; hg19: chr6-27474657;