6-95970099-T-G

Variant names:

• chr6-95970099-T-G
• rs632630
• ENST00000658251.2:n.168+44828A>C

Variant summary

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

The ENST00000658251.2(ENSG00000287578):​n.168+44828A>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 151,538 control chromosomes in the GnomAD database, including 68,659 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 (68659 hom., cov: 31)
• Consequence: ENSG00000287578 ENST00000658251.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 1 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 = 0.975 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.168+44828A>C		intron	N/A
	ENSG00000287578	ENST00000668456.1		n.105+45188A>C		intron	N/A
	ENSG00000287578	ENST00000780318.1		n.112+45188A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144085 AN: 151420 Hom.: 68603 Cov.: 31

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.952 AC: 144200 AN: 151538 Hom.: 68659 Cov.: 31 AF XY: 0.949 AC XY: 70306 AN XY: 74068

African (AFR) AF: 0.983 AC: 40770 AN: 41464

American (AMR) AF: 0.944 AC: 14284 AN: 15134

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3193 AN: 3454

East Asian (EAS) AF: 0.895 AC: 4591 AN: 5132

South Asian (SAS) AF: 0.868 AC: 4185 AN: 4820

European-Finnish (FIN) AF: 0.945 AC: 10015 AN: 10596

Middle Eastern (MID) AF: 0.836 AC: 244 AN: 292

European-Non Finnish (NFE) AF: 0.948 AC: 64104 AN: 67642

Other (OTH) AF: 0.930 AC: 1948 AN: 2094

Alfa AF: 0.949 Hom.: 3554

Bravo AF: 0.954

Asia WGS AF: 0.882 AC: 3061 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.18
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs632630;

hg19: chr6-96417975;