ENST00000658251.2:n.169-37124T>G

Variant names:

• chr6-95961274-A-C
• rs10484742
• ENST00000658251.2:n.169-37124T>G

Variant summary

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

The ENST00000658251.2(ENSG00000287578):​n.169-37124T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.03 in 151,634 control chromosomes in the GnomAD database, including 207 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 0.030 (207 hom., cov: 32)
• Consequence: ENSG00000287578 ENST00000658251.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986626	XR_001744263.2	n.148-37124T>G		intron_variant	Intron 1 of 2
LOC107986626	XR_001744264.2	n.148-37124T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287578	ENST00000658251.2	n.169-37124T>G		intron_variant	Intron 2 of 3
ENSG00000287578	ENST00000668456.1	n.106-37124T>G		intron_variant	Intron 1 of 2
ENSG00000287578	ENST00000780318.1	n.113-37124T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0300 AC: 4541 AN: 151516 Hom.: 204 Cov.: 32

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0113

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0279

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

GnomAD4 genome AF: 0.0300 AC: 4546 AN: 151634 Hom.: 207 Cov.: 32 AF XY: 0.0327 AC XY: 2423 AN XY: 74100

African (AFR) AF: 0.0149 AC: 617 AN: 41482

American (AMR) AF: 0.126 AC: 1905 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.0113 AC: 39 AN: 3454

East Asian (EAS) AF: 0.110 AC: 562 AN: 5124

South Asian (SAS) AF: 0.0738 AC: 356 AN: 4822

European-Finnish (FIN) AF: 0.0188 AC: 200 AN: 10614

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0117 AC: 793 AN: 67670

Other (OTH) AF: 0.0276 AC: 58 AN: 2098

Alfa AF: 0.0240 Hom.: 94

Bravo AF: 0.0389

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.0
DANN	Benign	0.47
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs10484742; hg19: chr6-96409150;