chr1-60273629-A-G

Variant names:

• chr1-60273629-A-G
• rs10493281
• ENST00000834475.1:n.255+3086T>C

Variant summary

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

The ENST00000834475.1(ENSG00000308475):​n.255+3086T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,208 control chromosomes in the GnomAD database, including 1,141 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 0.11 (1141 hom., cov: 32)
• Consequence: ENSG00000308475 ENST00000834475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 2 publications found

Genes affected

ENSG00000308475 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834475.1. 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
	ENSG00000308475	ENST00000834475.1		n.255+3086T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16892 AN: 152090 Hom.: 1142 Cov.: 32

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0819

Gnomad EAS AF: 0.0644

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.111 AC: 16889 AN: 152208 Hom.: 1141 Cov.: 32 AF XY: 0.110 AC XY: 8176 AN XY: 74416

African (AFR) AF: 0.0306 AC: 1273 AN: 41576

American (AMR) AF: 0.121 AC: 1854 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0819 AC: 284 AN: 3468

East Asian (EAS) AF: 0.0642 AC: 333 AN: 5186

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4820

European-Finnish (FIN) AF: 0.123 AC: 1301 AN: 10602

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10494 AN: 67966

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.139 Hom.: 3086

Bravo AF: 0.104

Asia WGS AF: 0.131 AC: 452 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.9
DANN	Benign	0.87
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs10493281; hg19: chr1-60739301; COSMIC: COSV53425345;