1-206893038-C-T

Position:

• chr1-206893038-C-T

Variant summary

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

The XR_007066836.1(LOC105372879):​n.125+2956G>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 0.466 in 152,000 control chromosomes in the GnomAD database, including 16,983 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 0.47 (16983 hom., cov: 32)
• Consequence: LOC105372879 XR_007066836.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

Genes affected

LOC105372879 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372879	XR_007066836.1	n.125+2956G>A		intron_variant, non_coding_transcript_variant
LOC105372879	XR_007066835.1	n.126-1353G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70708 AN: 151882 Hom.: 16967 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.466 AC: 70779 AN: 152000 Hom.: 16983 Cov.: 32 AF XY: 0.457 AC XY: 33951 AN XY: 74288

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.495

Alfa AF: 0.477 Hom.: 2458

Bravo AF: 0.477

Asia WGS AF: 0.271 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.34
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4845147; hg19: chr1-207066383;