chr12-93991936-G-A

Variant names:

• chr12-93991936-G-A
• rs2971589
• ENST00000786429.1:n.196+4396C>T

Variant summary

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

The ENST00000786429.1(ENSG00000257283):​n.196+4396C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,196 control chromosomes in the GnomAD database, including 2,130 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 0.16 (2130 hom., cov: 32)
• Consequence: ENSG00000257283 ENST00000786429.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 1 publications found

Genes affected

ENSG00000257283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369912	XR_001749263.2	n.161+4396C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257283	ENST00000786429.1	n.196+4396C>T		intron_variant	Intron 2 of 3
ENSG00000257283	ENST00000786430.1	n.207+4396C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24796 AN: 152078 Hom.: 2132 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0269

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.163 AC: 24789 AN: 152196 Hom.: 2130 Cov.: 32 AF XY: 0.159 AC XY: 11798 AN XY: 74422

African (AFR) AF: 0.161 AC: 6679 AN: 41518

American (AMR) AF: 0.116 AC: 1778 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 845 AN: 3470

East Asian (EAS) AF: 0.0266 AC: 138 AN: 5192

South Asian (SAS) AF: 0.143 AC: 691 AN: 4824

European-Finnish (FIN) AF: 0.167 AC: 1764 AN: 10586

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12369 AN: 67994

Other (OTH) AF: 0.179 AC: 378 AN: 2114

Alfa AF: 0.177 Hom.: 6955

Bravo AF: 0.159

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.73
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs2971589; hg19: chr12-94385712;