rs12068753

Variant names:

• chr1-159722747-T-A
• rs12068753
• ENST00000751816.1:n.108-3780T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-159722747-T-A
• chr1-159722747-T-C

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-3780T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,170 control chromosomes in the GnomAD database, including 2,757 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 0.15 (2757 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762
• Publications: 20 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) 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
ENSG00000297913	ENST00000751816.1	n.108-3780T>A		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-3780T>A		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-3780T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22150 AN: 152052 Hom.: 2745 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.146 AC: 22194 AN: 152170 Hom.: 2757 Cov.: 32 AF XY: 0.144 AC XY: 10735 AN XY: 74404

African (AFR) AF: 0.337 AC: 13993 AN: 41470

American (AMR) AF: 0.0803 AC: 1228 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3468

East Asian (EAS) AF: 0.152 AC: 786 AN: 5172

South Asian (SAS) AF: 0.109 AC: 527 AN: 4822

European-Finnish (FIN) AF: 0.0653 AC: 692 AN: 10596

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4177 AN: 68026

Other (OTH) AF: 0.137 AC: 290 AN: 2114

Alfa AF: 0.105 Hom.: 206

Bravo AF: 0.154

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.88
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs12068753; hg19: chr1-159692537;