rs6925466

Variant names:

• chr6-95928967-C-T
• rs6925466
• ENST00000658251.2:n.169-4817G>A

Variant summary

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

The ENST00000658251.2(ENSG00000287578):​n.169-4817G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,982 control chromosomes in the GnomAD database, including 7,510 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 0.28 (7510 hom., cov: 31)
• Consequence: ENSG00000287578 ENST00000658251.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787
• Publications: 2 publications found

Genes affected

ENSG00000287578 (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 (NFE) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658251.2. 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
	ENSG00000287578	ENST00000658251.2		n.169-4817G>A		intron	N/A
	ENSG00000287578	ENST00000668456.1		n.106-4817G>A		intron	N/A
	ENSG00000287578	ENST00000780318.1		n.113-4817G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43201 AN: 151864 Hom.: 7510 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.284 AC: 43195 AN: 151982 Hom.: 7510 Cov.: 31 AF XY: 0.279 AC XY: 20700 AN XY: 74256

African (AFR) AF: 0.101 AC: 4179 AN: 41486

American (AMR) AF: 0.271 AC: 4135 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1275 AN: 3472

East Asian (EAS) AF: 0.106 AC: 548 AN: 5178

South Asian (SAS) AF: 0.235 AC: 1130 AN: 4812

European-Finnish (FIN) AF: 0.347 AC: 3649 AN: 10512

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27179 AN: 67934

Other (OTH) AF: 0.314 AC: 664 AN: 2112

Alfa AF: 0.366 Hom.: 5327

Bravo AF: 0.271

Asia WGS AF: 0.181 AC: 629 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.9
DANN	Benign	0.69
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs6925466; hg19: chr6-96376843; COSMIC: COSV60251866;