6-167109907-A-G

Variant names:

• chr6-167109907-A-G
• rs6907666
• ENST00000705249.1:c.1066-26131A>G

Variant summary

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

The ENST00000705249.1(ENSG00000272980):​c.1066-26131A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,996 control chromosomes in the GnomAD database, including 26,982 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 0.60 (26982 hom., cov: 32)
• Consequence: ENSG00000272980 ENST00000705249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807
• Publications: 26 publications found

Genes affected

ENSG00000272980 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.629 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
ENSG00000272980	ENST00000705249.1	c.1066-26131A>G		intron_variant	Intron 11 of 12			ENSP00000516101.1

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90400 AN: 151876 Hom.: 26934 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.595 AC: 90510 AN: 151996 Hom.: 26982 Cov.: 32 AF XY: 0.596 AC XY: 44241 AN XY: 74292

African (AFR) AF: 0.574 AC: 23805 AN: 41438

American (AMR) AF: 0.640 AC: 9769 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2126 AN: 3472

East Asian (EAS) AF: 0.544 AC: 2815 AN: 5170

South Asian (SAS) AF: 0.611 AC: 2945 AN: 4818

European-Finnish (FIN) AF: 0.616 AC: 6504 AN: 10554

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40409 AN: 67958

Other (OTH) AF: 0.620 AC: 1306 AN: 2108

Alfa AF: 0.594 Hom.: 24740

Bravo AF: 0.598

Asia WGS AF: 0.600 AC: 2082 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	1.3
DANN	Benign	0.39
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs6907666; hg19: chr6-167523395;