rs12219246

chr10-102853598-A-Gchr10-102853598-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000631443.1(ENSG00000282772):n.259+657T>C 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 0.375 in 148,672 control chromosomes in the GnomAD database, including 10,671 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 (10671 hom., cov: 29)
• Consequence: ENST00000631443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000631443.1	n.259+657T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000440461.3	n.258+657T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000629474.2	n.259+657T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000632794.1	n.259+657T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.375 AC: 55720 AN: 148642 Hom.: 10672 Cov.: 29

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.375 AC: 55727 AN: 148672 Hom.: 10671 Cov.: 29 AF XY: 0.373 AC XY: 27083 AN XY: 72530

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.387

Alfa AF: 0.381 Hom.: 1396

Bravo AF: 0.382

Asia WGS AF: 0.452 AC: 1566 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.17
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12219246; hg19: chr10-104613355;