rs10859871

Positions:

• 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, non coding transcript 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: ENST00000636165.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.96

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000636165.1	n.1059-6646T>G		intron_variant, non_coding_transcript_variant

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;