rs10506338

Variant names:

• chr12-55035697-T-C
• rs10506338
• XR_245987.4:n.60A>G

Variant summary

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

The XR_245987.4(LOC101927484):​n.60A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0614 in 152,268 control chromosomes in the GnomAD database, including 720 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 0.061 (720 hom., cov: 32)
• Consequence: LOC101927484 XR_245987.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.915

Genes affected

LOC101927484 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927484	XR_245987.4	n.60A>G		non_coding_transcript_exon_variant	Exon 1 of 5
LOC101927484	XR_245988.3	n.44A>G		non_coding_transcript_exon_variant	Exon 1 of 6
LOC101927484	XR_944985.1	n.44A>G		non_coding_transcript_exon_variant	Exon 1 of 5
LOC101927484	XR_944986.1	n.44A>G		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0613 AC: 9334 AN: 152150 Hom.: 721 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0403

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0614 AC: 9346 AN: 152268 Hom.: 720 Cov.: 32 AF XY: 0.0591 AC XY: 4398 AN XY: 74458

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.0403

Gnomad4 ASJ AF: 0.0585

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.0000941

Gnomad4 NFE AF: 0.0121

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0342 Hom.: 93

Bravo AF: 0.0699

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506338; hg19: chr12-55429481;