rs517258

Variant names:

• chr7-65278280-T-G
• rs517258
• ENST00000632111.1:n.165+8742T>G

Variant summary

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

The ENST00000632111.1(ENSG00000282381):​n.165+8742T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,868 control chromosomes in the GnomAD database, including 11,093 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 0.38 (11093 hom., cov: 31)
• Consequence: ENSG00000282381 ENST00000632111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883
• Publications: 16 publications found

Genes affected

ENSG00000282381 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375334	XR_001744935.2	n.165+8742T>G		intron_variant	Intron 1 of 4
LOC105375334	XR_001744938.2	n.165+8742T>G		intron_variant	Intron 1 of 6
LOC105375334	XR_007060360.1	n.165+8742T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282381	ENST00000632111.1	n.165+8742T>G		intron_variant	Intron 1 of 2	2
ENSG00000282381	ENST00000685802.2	n.234+8742T>G		intron_variant	Intron 1 of 2
ENSG00000282381	ENST00000687368.2	n.201+8742T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57439 AN: 151750 Hom.: 11078 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.379 AC: 57489 AN: 151868 Hom.: 11093 Cov.: 31 AF XY: 0.374 AC XY: 27764 AN XY: 74224

African (AFR) AF: 0.410 AC: 16996 AN: 41410

American (AMR) AF: 0.294 AC: 4479 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1070 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1947 AN: 5160

South Asian (SAS) AF: 0.401 AC: 1928 AN: 4812

European-Finnish (FIN) AF: 0.339 AC: 3572 AN: 10550

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26327 AN: 67914

Other (OTH) AF: 0.365 AC: 768 AN: 2104

Alfa AF: 0.378 Hom.: 2925

Bravo AF: 0.374

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.2
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs517258; hg19: chr7-64743183;