rs12061304

Variant names:

• chr1-110695063-A-G
• rs12061304
• ENST00000768410.1:n.219-26462A>G

Variant summary

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

The ENST00000768410.1(ENSG00000300042):​n.219-26462A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,990 control chromosomes in the GnomAD database, including 7,192 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 0.30 (7192 hom., cov: 31)
• Consequence: ENSG00000300042 ENST00000768410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 13 publications found

Genes affected

ENSG00000300042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 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
ENSG00000300042	ENST00000768410.1	n.219-26462A>G		intron_variant	Intron 1 of 1
ENSG00000300042	ENST00000768411.1	n.386+489A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45464 AN: 151872 Hom.: 7191 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0746

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.299 AC: 45481 AN: 151990 Hom.: 7192 Cov.: 31 AF XY: 0.289 AC XY: 21474 AN XY: 74272

African (AFR) AF: 0.332 AC: 13750 AN: 41442

American (AMR) AF: 0.208 AC: 3178 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3470

East Asian (EAS) AF: 0.0747 AC: 387 AN: 5178

South Asian (SAS) AF: 0.208 AC: 1003 AN: 4812

European-Finnish (FIN) AF: 0.262 AC: 2773 AN: 10578

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22899 AN: 67934

Other (OTH) AF: 0.270 AC: 569 AN: 2108

Alfa AF: 0.313 Hom.: 34539

Bravo AF: 0.291

Asia WGS AF: 0.127 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.65
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs12061304; hg19: chr1-111237685;