6-166292681-A-G

Variant names:

• chr6-166292681-A-G
• rs6915183
• ENST00000722405.1:n.140-1324A>G

Variant summary

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

The ENST00000722405.1(ENSG00000294280):​n.140-1324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,164 control chromosomes in the GnomAD database, including 32,755 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 0.65 (32755 hom., cov: 34)
• Consequence: ENSG00000294280 ENST00000722405.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 8 publications found

Genes affected

ENSG00000294280 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 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
ENSG00000294280	ENST00000722405.1	n.140-1324A>G		intron_variant	Intron 1 of 1
ENSG00000294280	ENST00000722406.1	n.241-1324A>G		intron_variant	Intron 1 of 1
ENSG00000294280	ENST00000722407.1	n.131-1164A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98953 AN: 152046 Hom.: 32712 Cov.: 34

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.651 AC: 99053 AN: 152164 Hom.: 32755 Cov.: 34 AF XY: 0.652 AC XY: 48519 AN XY: 74388

African (AFR) AF: 0.712 AC: 29581 AN: 41538

American (AMR) AF: 0.611 AC: 9346 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2688 AN: 3466

East Asian (EAS) AF: 0.904 AC: 4667 AN: 5164

South Asian (SAS) AF: 0.731 AC: 3530 AN: 4832

European-Finnish (FIN) AF: 0.571 AC: 6037 AN: 10568

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40925 AN: 67984

Other (OTH) AF: 0.682 AC: 1442 AN: 2114

Alfa AF: 0.630 Hom.: 84668

Bravo AF: 0.656

Asia WGS AF: 0.806 AC: 2804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs6915183; hg19: chr6-166706169; COSMIC: COSV64568418;