rs1860487

Variant names:

• chr7-124075082-T-C
• rs1860487
• ENST00000484322.5:n.168+25858T>C

Variant summary

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

The ENST00000484322.5(ENSG00000242593):​n.168+25858T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,844 control chromosomes in the GnomAD database, including 17,773 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 0.48 (17773 hom., cov: 32)
• Consequence: ENSG00000242593 ENST00000484322.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 4 publications found

Genes affected

ENSG00000242593 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000242593	ENST00000484322.5	n.168+25858T>C		intron_variant	Intron 2 of 8	1
ENSG00000242593	ENST00000650961.1	n.290-2165T>C		intron_variant	Intron 2 of 10
ENSG00000242593	ENST00000651674.1	n.93+25858T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72946 AN: 151726 Hom.: 17758 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.481 AC: 73002 AN: 151844 Hom.: 17773 Cov.: 32 AF XY: 0.481 AC XY: 35729 AN XY: 74208

African (AFR) AF: 0.518 AC: 21438 AN: 41408

American (AMR) AF: 0.495 AC: 7559 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3468

East Asian (EAS) AF: 0.247 AC: 1275 AN: 5160

South Asian (SAS) AF: 0.469 AC: 2259 AN: 4816

European-Finnish (FIN) AF: 0.516 AC: 5448 AN: 10554

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.471 AC: 31943 AN: 67874

Other (OTH) AF: 0.475 AC: 1000 AN: 2106

Alfa AF: 0.476 Hom.: 9853

Bravo AF: 0.480

Asia WGS AF: 0.374 AC: 1301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.43
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs1860487; hg19: chr7-123715136;