6-95970099-T-G

Variant names:

• chr6-95970099-T-G
• rs632630
• ENST00000658251.1:n.75+44828A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658251.1(ENSG00000287578):​n.75+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 ENST00000658251.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

ENSG00000287578 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986626	XR_001744263.2	n.147+45188A>C		intron_variant	Intron 1 of 2
LOC107986626	XR_001744264.2	n.147+45188A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287578	ENST00000658251.1	n.75+44828A>C		intron_variant	Intron 1 of 2
ENSG00000287578	ENST00000668456.1	n.105+45188A>C		intron_variant	Intron 1 of 2

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

Gnomad4 AFR AF: 0.983

Gnomad4 AMR AF: 0.944

Gnomad4 ASJ AF: 0.924

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.948

Gnomad4 OTH AF: 0.930

Alfa AF: 0.945 Hom.: 3176

Bravo AF: 0.954

Asia WGS AF: 0.882 AC: 3061 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs632630; hg19: chr6-96417975;