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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000632111.1. 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
	ENSG00000282381	ENST00000632111.1	TSL:2	n.165+8742T>G		intron	N/A
	ENSG00000282381	ENST00000685802.2		n.234+8742T>G		intron	N/A
	ENSG00000282381	ENST00000687368.2		n.201+8742T>G		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs517258;

hg19: chr7-64743183;