1-160735829-T-C

Position:

• chr1-160735829-T-C

Variant summary

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

The XR_007066687.1(LOC124904440):​n.78-1576A>G 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 0.809 in 144,856 control chromosomes in the GnomAD database, including 47,771 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 0.81 (47771 hom., cov: 23)
• Consequence: LOC124904440 XR_007066687.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

LOC124904440 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904440	XR_007066687.1	n.78-1576A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.809 AC: 117097 AN: 144736 Hom.: 47733 Cov.: 23

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.809 AC: 117192 AN: 144856 Hom.: 47771 Cov.: 23 AF XY: 0.809 AC XY: 56330 AN XY: 69590

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.834

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.822

Alfa AF: 0.825 Hom.: 63436

Bravo AF: 0.813

Asia WGS AF: 0.929 AC: 3233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs549471; hg19: chr1-160705619;