rs12660854

Variant names:

• chr6-94689423-T-G
• rs12660854
• ENST00000689670.1:n.529+662A>C

Variant summary

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

The ENST00000689670.1(ENSG00000289178):​n.529+662A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,952 control chromosomes in the GnomAD database, including 1,883 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 0.14 (1883 hom., cov: 32)
• Consequence: ENSG00000289178 ENST00000689670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 3 publications found

Genes affected

ENSG00000289178 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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
ENSG00000289178	ENST00000689670.1	n.529+662A>C		intron_variant	Intron 3 of 9
ENSG00000289178	ENST00000701797.1	n.295+662A>C		intron_variant	Intron 2 of 9
ENSG00000289178	ENST00000834925.1	n.366+662A>C		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21693 AN: 151836 Hom.: 1873 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.143 AC: 21733 AN: 151952 Hom.: 1883 Cov.: 32 AF XY: 0.148 AC XY: 11003 AN XY: 74238

African (AFR) AF: 0.169 AC: 6987 AN: 41454

American (AMR) AF: 0.205 AC: 3131 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1659 AN: 5126

South Asian (SAS) AF: 0.241 AC: 1161 AN: 4820

European-Finnish (FIN) AF: 0.124 AC: 1306 AN: 10526

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.100 AC: 6811 AN: 67986

Other (OTH) AF: 0.139 AC: 292 AN: 2108

Alfa AF: 0.123 Hom.: 1227

Bravo AF: 0.150

Asia WGS AF: 0.289 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.23
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12660854; hg19: chr6-95399141;