ENST00000648816.1:n.107-10779A>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000285703 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285703	ENST00000648816.1		n.107-10779A>G		intron	N/A
	ENSG00000286652	ENST00000779964.1		n.280-6518T>C		intron	N/A
	ENSG00000286652	ENST00000779965.1		n.276-8089T>C		intron	N/A

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

African (AFR) AF: 0.0124 AC: 514 AN: 41564

American (AMR) AF: 0.0328 AC: 502 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3466

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5184

South Asian (SAS) AF: 0.0214 AC: 103 AN: 4818

European-Finnish (FIN) AF: 0.103 AC: 1097 AN: 10618

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0730 AC: 4968 AN: 68022

Other (OTH) AF: 0.0345 AC: 73 AN: 2116

Alfa AF: 0.0611 Hom.: 648

Bravo AF: 0.0430

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	16
DANN	Benign	0.82
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs12189640; hg19: chr6-27474657;