rs12660854

chr6-94689423-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000701797.1(ENSG00000289178):n.295+662A>C variant causes a intron, non coding transcript 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: ENST00000701797.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701797.1	n.295+662A>C		intron_variant, non_coding_transcript_variant
	ENST00000689670.1	n.529+662A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.139

Alfa AF: 0.116 Hom.: 758

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12660854; hg19: chr6-95399141;