rs704144

Variant names:

• chr12-91258901-G-A
• rs704144
• ENST00000747678.1:n.163-1761C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-91258901-G-A
• chr12-91258901-G-T

Variant summary

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

The ENST00000747678.1(ENSG00000297389):​n.163-1761C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 151,284 control chromosomes in the GnomAD database, including 52,973 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 0.83 (52973 hom., cov: 27)
• Consequence: ENSG00000297389 ENST00000747678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 4 publications found

Genes affected

ENSG00000297389 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.908 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
ENSG00000297389	ENST00000747678.1	n.163-1761C>T		intron_variant	Intron 2 of 4
ENSG00000297389	ENST00000747679.1	n.66-1761C>T		intron_variant	Intron 1 of 3
ENSG00000297389	ENST00000747680.1	n.167-342C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.832 AC: 125845 AN: 151172 Hom.: 52955 Cov.: 27

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.832 AC: 125914 AN: 151284 Hom.: 52973 Cov.: 27 AF XY: 0.837 AC XY: 61875 AN XY: 73926

African (AFR) AF: 0.696 AC: 28594 AN: 41108

American (AMR) AF: 0.861 AC: 13052 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2851 AN: 3458

East Asian (EAS) AF: 0.846 AC: 4333 AN: 5122

South Asian (SAS) AF: 0.931 AC: 4469 AN: 4800

European-Finnish (FIN) AF: 0.923 AC: 9710 AN: 10518

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60215 AN: 67814

Other (OTH) AF: 0.834 AC: 1754 AN: 2104

Alfa AF: 0.868 Hom.: 216806

Bravo AF: 0.818

Asia WGS AF: 0.875 AC: 3038 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.15
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs704144; hg19: chr12-91652678;