chr12-95318100-A-C

Variant names:

• chr12-95318100-A-C
• rs10859871
• ENST00000636165.1:n.1059-6646T>G

Variant summary

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

The ENST00000636165.1(ENSG00000257943):​n.1059-6646T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,014 control chromosomes in the GnomAD database, including 11,312 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 0.37 (11312 hom., cov: 31)
• Consequence: ENSG00000257943 ENST00000636165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.96
• Publications: 48 publications found

Genes affected

ENSG00000257943 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636165.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257943	ENST00000636165.1	TSL:6	n.1059-6646T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56399 AN: 151896 Hom.: 11283 Cov.: 31

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.372 AC: 56484 AN: 152014 Hom.: 11312 Cov.: 31 AF XY: 0.366 AC XY: 27170 AN XY: 74312

African (AFR) AF: 0.532 AC: 22034 AN: 41424

American (AMR) AF: 0.334 AC: 5097 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1413 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1378 AN: 5172

South Asian (SAS) AF: 0.410 AC: 1970 AN: 4810

European-Finnish (FIN) AF: 0.210 AC: 2227 AN: 10586

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20979 AN: 67964

Other (OTH) AF: 0.393 AC: 827 AN: 2106

Alfa AF: 0.336 Hom.: 17847

Bravo AF: 0.387

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.52
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs10859871; hg19: chr12-95711876;