rs12030600

Variant names:

• chr1-231469633-G-A
• rs12030600
• ENST00000662216.1:c.-207-6959C>T

Variant summary

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

The ENST00000662216.1(ENSG00000287856):​c.-207-6959C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,054 control chromosomes in the GnomAD database, including 1,704 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 0.12 (1704 hom., cov: 32)
• Consequence: ENSG00000287856 ENST00000662216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 3 publications found

Genes affected

ENSG00000287856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 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
ENSG00000287856	ENST00000662216.1	c.-207-6959C>T		intron_variant	Intron 2 of 6			ENSP00000499467.1
ENSG00000287856	ENST00000653908.1	c.-207-6959C>T		intron_variant	Intron 1 of 4			ENSP00000499669.1
ENSG00000287856	ENST00000653198.1	n.230+5397C>T		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18338 AN: 151936 Hom.: 1696 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0795

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.121 AC: 18363 AN: 152054 Hom.: 1704 Cov.: 32 AF XY: 0.125 AC XY: 9312 AN XY: 74338

African (AFR) AF: 0.195 AC: 8091 AN: 41470

American (AMR) AF: 0.118 AC: 1805 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0795 AC: 276 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2317 AN: 5164

South Asian (SAS) AF: 0.234 AC: 1127 AN: 4818

European-Finnish (FIN) AF: 0.0568 AC: 601 AN: 10572

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3844 AN: 67972

Other (OTH) AF: 0.125 AC: 264 AN: 2110

Alfa AF: 0.0835 Hom.: 1704

Bravo AF: 0.127

Asia WGS AF: 0.315 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.8
DANN	Benign	0.86
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs12030600; hg19: chr1-231605379;