rs10282458

Variant names:

• chr7-150348213-G-A
• rs10282458
• ENST00000782371.1:n.371G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-150348213-G-A
• chr7-150348213-G-T

Variant summary

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

The ENST00000782371.1(ENSG00000301866):​n.371G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,072 control chromosomes in the GnomAD database, including 5,229 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 0.26 (5229 hom., cov: 32)
• Consequence: ENSG00000301866 ENST00000782371.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 38 publications found

Genes affected

ENSG00000301866 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986858	XR_001745420.3	n.607+4572G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301866	ENST00000782371.1	n.371G>A		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000301866	ENST00000782368.1	n.256+4572G>A		intron_variant	Intron 1 of 1
ENSG00000301866	ENST00000782369.1	n.239+4572G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39519 AN: 151954 Hom.: 5225 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.260 AC: 39552 AN: 152072 Hom.: 5229 Cov.: 32 AF XY: 0.259 AC XY: 19262 AN XY: 74324

African (AFR) AF: 0.280 AC: 11638 AN: 41492

American (AMR) AF: 0.167 AC: 2558 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1115 AN: 3468

East Asian (EAS) AF: 0.287 AC: 1478 AN: 5150

South Asian (SAS) AF: 0.305 AC: 1469 AN: 4818

European-Finnish (FIN) AF: 0.251 AC: 2656 AN: 10570

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17707 AN: 67970

Other (OTH) AF: 0.235 AC: 496 AN: 2112

Alfa AF: 0.261 Hom.: 22980

Bravo AF: 0.254

Asia WGS AF: 0.295 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.9
DANN	Benign	0.69
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs10282458; hg19: chr7-150045302;