1-34485995-C-T

Position:

• chr1-34485995-C-T

Variant summary

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

The XR_001737964.2(LOC105378641):​n.578-16009G>A 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 0.608 in 152,022 control chromosomes in the GnomAD database, including 28,819 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 0.61 (28819 hom., cov: 32)
• Consequence: LOC105378641 XR_001737964.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

Genes affected

LOC105378641 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378641	XR_001737964.2	n.578-16009G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92318 AN: 151904 Hom.: 28791 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.608 AC: 92391 AN: 152022 Hom.: 28819 Cov.: 32 AF XY: 0.617 AC XY: 45855 AN XY: 74276

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.608

Alfa AF: 0.601 Hom.: 7105

Bravo AF: 0.602

Asia WGS AF: 0.819 AC: 2845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3905173; hg19: chr1-34951596;