rs12641251

chr4-144503691-G-Achr4-144503691-G-C

Variant summary

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

The XR_939273.3(LOC105377462):n.164+58293C>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 0.581 in 151,938 control chromosomes in the GnomAD database, including 27,306 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 0.58 (27306 hom., cov: 32)
• Consequence: LOC105377462 XR_939273.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

LOC105377462 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377462	XR_939273.3	n.164+58293C>T		intron_variant, non_coding_transcript_variant
LOC105377462	XR_939272.3	n.165-4171C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648340.1	n.138+5550C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88184 AN: 151820 Hom.: 27282 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.581 AC: 88244 AN: 151938 Hom.: 27306 Cov.: 32 AF XY: 0.583 AC XY: 43303 AN XY: 74248

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.592

Alfa AF: 0.659 Hom.: 42319

Bravo AF: 0.557

Asia WGS AF: 0.569 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.062
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12641251; hg19: chr4-145424843;