chr6-167092303-T-C

Variant names:

• chr6-167092303-T-C
• rs6902119
• ENST00000705249.1:c.1066-43735T>C

Variant summary

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

The ENST00000705249.1(ENSG00000272980):​c.1066-43735T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,978 control chromosomes in the GnomAD database, including 14,896 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 0.44 (14896 hom., cov: 32)
• Consequence: ENSG00000272980 ENST00000705249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 19 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272980	ENST00000705249.1		c.1066-43735T>C		intron	N/A	ENSP00000516101.1
	ENSG00000272980	ENST00000705250.1		c.844-43735T>C		intron	N/A	ENSP00000516102.1
	ENSG00000272980	ENST00000705254.1		c.673-43735T>C		intron	N/A	ENSP00000516106.1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66908 AN: 151862 Hom.: 14886 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.441 AC: 66955 AN: 151978 Hom.: 14896 Cov.: 32 AF XY: 0.441 AC XY: 32734 AN XY: 74268

African (AFR) AF: 0.468 AC: 19365 AN: 41420

American (AMR) AF: 0.385 AC: 5886 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1515 AN: 3466

East Asian (EAS) AF: 0.375 AC: 1925 AN: 5140

South Asian (SAS) AF: 0.492 AC: 2367 AN: 4814

European-Finnish (FIN) AF: 0.415 AC: 4378 AN: 10546

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30165 AN: 67990

Other (OTH) AF: 0.441 AC: 931 AN: 2112

Alfa AF: 0.436 Hom.: 24194

Bravo AF: 0.434

Asia WGS AF: 0.436 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.56
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs6902119; hg19: chr6-167505791;