7-45942861-T-C

Variant names:

• chr7-45942861-T-C
• rs2462686
• ENST00000658576.2:n.432+1981T>C

Variant summary

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

The ENST00000658576.2(ENSG00000237471):​n.432+1981T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,084 control chromosomes in the GnomAD database, including 6,344 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 0.28 (6344 hom., cov: 32)
• Consequence: ENSG00000237471 ENST00000658576.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 12 publications found

Genes affected

ENSG00000237471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658576.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC102723446	NR_187744.1		n.432+1981T>C		intron	N/A
	LOC102723446	NR_187745.1		n.432+1981T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237471	ENST00000658576.2		n.432+1981T>C		intron	N/A
	ENSG00000237471	ENST00000664963.2		n.432+1981T>C		intron	N/A
	ENSG00000237471	ENST00000797062.1		n.168+1981T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42725 AN: 151966 Hom.: 6334 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.0350

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.281 AC: 42774 AN: 152084 Hom.: 6344 Cov.: 32 AF XY: 0.277 AC XY: 20628 AN XY: 74346

African (AFR) AF: 0.246 AC: 10211 AN: 41508

American (AMR) AF: 0.240 AC: 3668 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3462

East Asian (EAS) AF: 0.0351 AC: 182 AN: 5190

South Asian (SAS) AF: 0.342 AC: 1646 AN: 4818

European-Finnish (FIN) AF: 0.256 AC: 2706 AN: 10562

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22199 AN: 67948

Other (OTH) AF: 0.302 AC: 638 AN: 2112

Alfa AF: 0.301 Hom.: 12267

Bravo AF: 0.275

Asia WGS AF: 0.225 AC: 781 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.33
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2462686; hg19: chr7-45982460;