rs10506546

chr12-67386525-T-G

Variant summary

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

The XR_945047.3(LOC105369813):n.60+1958A>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 0.113 in 152,224 control chromosomes in the GnomAD database, including 1,063 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 0.11 (1063 hom., cov: 32)
• Consequence: LOC105369813 XR_945047.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.41

Genes affected

LOC105369813 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369813	XR_945047.3	n.60+1958A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17224 AN: 152104 Hom.: 1062 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0947

Gnomad AMR AF: 0.0931

Gnomad ASJ AF: 0.0999

Gnomad EAS AF: 0.0723

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0514

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.113 AC: 17227 AN: 152224 Hom.: 1063 Cov.: 32 AF XY: 0.110 AC XY: 8192 AN XY: 74448

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.0930

Gnomad4 ASJ AF: 0.0999

Gnomad4 EAS AF: 0.0722

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0514

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.107

Alfa AF: 0.107 Hom.: 424

Bravo AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	13
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506546; hg19: chr12-67780305;