12-97129856-C-T

Variant names:

• chr12-97129856-C-T
• rs2193371
• ENST00000716365.1:n.206-55333C>T

Variant summary

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

The ENST00000716365.1(ENSG00000257470):​n.206-55333C>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 152,088 control chromosomes in the GnomAD database, including 1,556 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 (1556 hom., cov: 32)
• Consequence: ENSG00000257470 ENST00000716365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 2 publications found

Genes affected

ENSG00000257470 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716365.1. 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
	ENSG00000257470	ENST00000716365.1		n.206-55333C>T		intron	N/A
	ENSG00000257470	ENST00000716366.1		n.185-55220C>T		intron	N/A
	ENSG00000257470	ENST00000716367.1		n.55-55220C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18303 AN: 151970 Hom.: 1544 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0689

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0581

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.121 AC: 18351 AN: 152088 Hom.: 1556 Cov.: 32 AF XY: 0.122 AC XY: 9101 AN XY: 74356

African (AFR) AF: 0.221 AC: 9155 AN: 41462

American (AMR) AF: 0.175 AC: 2670 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3468

East Asian (EAS) AF: 0.125 AC: 647 AN: 5166

South Asian (SAS) AF: 0.122 AC: 590 AN: 4822

European-Finnish (FIN) AF: 0.0689 AC: 729 AN: 10576

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0580 AC: 3947 AN: 68004

Other (OTH) AF: 0.117 AC: 247 AN: 2112

Alfa AF: 0.0306 Hom.: 21

Bravo AF: 0.136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2193371;

hg19: chr12-97523634;