6-95962238-A-G

Variant names:

• chr6-95962238-A-G
• rs659115
• ENST00000658251.2:n.169-38088T>C

Variant summary

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

The ENST00000658251.2(ENSG00000287578):​n.169-38088T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 151,492 control chromosomes in the GnomAD database, including 68,654 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 0.95 (68654 hom., cov: 32)
• Consequence: ENSG00000287578 ENST00000658251.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 4 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287578	ENST00000658251.2		n.169-38088T>C		intron	N/A
	ENSG00000287578	ENST00000668456.1		n.106-38088T>C		intron	N/A
	ENSG00000287578	ENST00000780318.1		n.113-38088T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144055 AN: 151374 Hom.: 68598 Cov.: 32

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.952 AC: 144170 AN: 151492 Hom.: 68654 Cov.: 32 AF XY: 0.949 AC XY: 70280 AN XY: 74044

African (AFR) AF: 0.984 AC: 40781 AN: 41464

American (AMR) AF: 0.944 AC: 14290 AN: 15134

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3197 AN: 3458

East Asian (EAS) AF: 0.895 AC: 4598 AN: 5140

South Asian (SAS) AF: 0.867 AC: 4187 AN: 4828

European-Finnish (FIN) AF: 0.945 AC: 10022 AN: 10606

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64038 AN: 67570

Other (OTH) AF: 0.932 AC: 1945 AN: 2086

Alfa AF: 0.944 Hom.: 136149

Bravo AF: 0.954

Asia WGS AF: 0.883 AC: 3071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs659115; hg19: chr6-96410114;