rs12246221

chr10-42339981-A-Gchr10-42339981-A-T

Variant summary

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

The NR_024380.1(LOC441666):n.286+520T>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 0.21 in 152,050 control chromosomes in the GnomAD database, including 3,909 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 0.21 (3909 hom., cov: 33)
• Consequence: LOC441666 NR_024380.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC441666	NR_024380.1	n.286+520T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000423987.2	n.74-1741T>C		intron_variant, non_coding_transcript_variant
	ENST00000701816.1	n.178+27835T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31925 AN: 151932 Hom.: 3895 Cov.: 33

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0935

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.210 AC: 31969 AN: 152050 Hom.: 3909 Cov.: 33 AF XY: 0.206 AC XY: 15339 AN XY: 74338

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.0935

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.240

Alfa AF: 0.0898 Hom.: 125

Bravo AF: 0.221

Asia WGS AF: 0.336 AC: 1162 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.7
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12246221; hg19: chr10-42835429;