rs12136988

Variant names:

• chr1-58637536-C-G
• rs12136988
• ENST00000637377.2:n.161+61160C>G

Variant summary

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

The ENST00000767021.1(ENSG00000283445):​n.188+61160C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,042 control chromosomes in the GnomAD database, including 4,456 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 0.22 (4456 hom., cov: 33)
• Consequence: ENSG00000283445 ENST00000767021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 2 publications found

Genes affected

ENSG00000283445 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767021.1. 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
	ENSG00000283445	ENST00000637377.2	TSL:5	n.161+61160C>G		intron	N/A
	ENSG00000283445	ENST00000767021.1		n.188+61160C>G		intron	N/A
	ENSG00000283445	ENST00000767022.1		n.142+61160C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33066 AN: 151924 Hom.: 4453 Cov.: 33

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.217 AC: 33066 AN: 152042 Hom.: 4456 Cov.: 33 AF XY: 0.220 AC XY: 16330 AN XY: 74344

African (AFR) AF: 0.0548 AC: 2274 AN: 41498

American (AMR) AF: 0.258 AC: 3947 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 969 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1506 AN: 5178

South Asian (SAS) AF: 0.279 AC: 1346 AN: 4824

European-Finnish (FIN) AF: 0.245 AC: 2585 AN: 10548

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19538 AN: 67938

Other (OTH) AF: 0.250 AC: 528 AN: 2110

Alfa AF: 0.242 Hom.: 623

Bravo AF: 0.213

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		-0.47

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: rs12136988;

hg19: chr1-59103208;