rs10859871

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-95318100-A-C
• chr12-95318100-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000257943 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000257943	ENST00000636165.1	n.1059-6646T>G		intron_variant	Intron 7 of 7	6

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

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.393

Alfa AF: 0.310 Hom.: 3496

Bravo AF: 0.387

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10859871; hg19: chr12-95711876;