1-224887055-C-A

Position:

• chr1-224887055-C-A

Variant summary

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

The XR_949207.2(LOC105373109):​n.63-2274G>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 0.339 in 152,078 control chromosomes in the GnomAD database, including 10,594 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 0.34 (10594 hom., cov: 32)
• Consequence: LOC105373109 XR_949207.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

LOC105373109 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373109	XR_949207.2	n.63-2274G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51577 AN: 151960 Hom.: 10586 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.339 AC: 51589 AN: 152078 Hom.: 10594 Cov.: 32 AF XY: 0.344 AC XY: 25556 AN XY: 74316

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.345

Alfa AF: 0.239 Hom.: 629

Bravo AF: 0.330

Asia WGS AF: 0.508 AC: 1765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10737416; hg19: chr1-225074757;