rs74057236

Variant names:

• chr12-6962550-G-A
• rs74057236
• XR_931601.2:n.550C>T

Variant summary

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

The XR_931601.2(LOC105369634):​n.550C>T 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 0.0995 in 152,142 control chromosomes in the GnomAD database, including 899 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 0.10 (899 hom., cov: 33)
• Consequence: LOC105369634 XR_931601.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622

Genes affected

LOC105369634 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369634	XR_931601.2	n.550C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 15128 AN: 152024 Hom.: 899 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0905

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0995 AC: 15145 AN: 152142 Hom.: 899 Cov.: 33 AF XY: 0.0961 AC XY: 7145 AN XY: 74378

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0727

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.00136

Gnomad4 SAS AF: 0.0680

Gnomad4 FIN AF: 0.0730

Gnomad4 NFE AF: 0.0905

Gnomad4 OTH AF: 0.0733

Alfa AF: 0.0928 Hom.: 129

Bravo AF: 0.103

Asia WGS AF: 0.0440 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	18
DANN	Uncertain	0.98

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74057236; hg19: chr12-7071713;