rs1859441

Positions:

• chr12-48029450-C-T

Variant summary

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

The XR_001749115.3(LOC105369750):​n.227-321C>T 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 0.208 in 152,234 control chromosomes in the GnomAD database, including 3,781 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 (3781 hom., cov: 33)
• Consequence: LOC105369750 XR_001749115.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725

Genes affected

LOC105369750 (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 (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369750	XR_001749115.3	n.227-321C>T		intron_variant, non_coding_transcript_variant
LOC105369750	XR_001749116.3	n.168-321C>T		intron_variant, non_coding_transcript_variant
LOC105369750	XR_944904.3	n.227-321C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31584 AN: 152118 Hom.: 3775 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.208 AC: 31620 AN: 152234 Hom.: 3781 Cov.: 33 AF XY: 0.215 AC XY: 16019 AN XY: 74412

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.208

Alfa AF: 0.172 Hom.: 3125

Bravo AF: 0.217

Asia WGS AF: 0.375 AC: 1301 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	0.36
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1859441; hg19: chr12-48423233;