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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782371.1. 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
	ENSG00000301866	ENST00000782371.1		n.371G>A		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000301866	ENST00000782368.1		n.256+4572G>A		intron	N/A
	ENSG00000301866	ENST00000782369.1		n.239+4572G>A		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs10282458;

hg19: chr7-150045302;