rs10506547

Positions:

• chr12-67415454-A-G
• chr12-67415454-A-T

Variant summary

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

The XR_001749186.2(LOC105369812):​n.500-5703A>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 0.763 in 152,132 control chromosomes in the GnomAD database, including 44,774 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 0.76 (44774 hom., cov: 32)
• Consequence: LOC105369812 XR_001749186.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

LOC105369812 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369812	XR_001749186.2	n.500-5703A>G		intron_variant, non_coding_transcript_variant
LOC105369812	XR_945043.3	n.500-5703A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115897 AN: 152014 Hom.: 44716 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.763 AC: 116017 AN: 152132 Hom.: 44774 Cov.: 32 AF XY: 0.755 AC XY: 56125 AN XY: 74348

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.756

Alfa AF: 0.761 Hom.: 6617

Bravo AF: 0.760

Asia WGS AF: 0.575 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.75
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506547; hg19: chr12-67809234;