chr6-167089150-A-C

Variant names:

• chr6-167089150-A-C
• rs1331301
• ENST00000705249.1:c.1066-46888A>C

Variant summary

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

The ENST00000705249.1(ENSG00000272980):​c.1066-46888A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,050 control chromosomes in the GnomAD database, including 9,592 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 0.33 (9592 hom., cov: 32)
• Consequence: ENSG00000272980 ENST00000705249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 12 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000705249.1. 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
	ENSG00000272980	ENST00000705249.1		c.1066-46888A>C		intron	N/A	ENSP00000516101.1
	ENSG00000272980	ENST00000705250.1		c.844-46888A>C		intron	N/A	ENSP00000516102.1
	ENSG00000272980	ENST00000705254.1		c.673-46888A>C		intron	N/A	ENSP00000516106.1

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50769 AN: 151930 Hom.: 9589 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.334 AC: 50785 AN: 152050 Hom.: 9592 Cov.: 32 AF XY: 0.337 AC XY: 25062 AN XY: 74302

African (AFR) AF: 0.149 AC: 6203 AN: 41530

American (AMR) AF: 0.457 AC: 6980 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1422 AN: 3470

East Asian (EAS) AF: 0.420 AC: 2171 AN: 5168

South Asian (SAS) AF: 0.374 AC: 1805 AN: 4822

European-Finnish (FIN) AF: 0.415 AC: 4372 AN: 10532

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26485 AN: 67944

Other (OTH) AF: 0.368 AC: 778 AN: 2112

Alfa AF: 0.365 Hom.: 26927

Bravo AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.030
DANN	Benign	0.23
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1331301; hg19: chr6-167502638;