chr1-160400029-T-G

Position:

• chr1-160400029-T-G

Variant summary

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

The XR_007066686.1(LOC105371466):​n.481+6143A>C 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 0.313 in 152,028 control chromosomes in the GnomAD database, including 7,879 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 0.31 (7879 hom., cov: 32)
• Consequence: LOC105371466 XR_007066686.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

Genes affected

LOC105371466 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371466	XR_007066686.1	n.481+6143A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47545 AN: 151910 Hom.: 7881 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.313 AC: 47562 AN: 152028 Hom.: 7879 Cov.: 32 AF XY: 0.312 AC XY: 23197 AN XY: 74326

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.324

Alfa AF: 0.325 Hom.: 2431

Bravo AF: 0.316

Asia WGS AF: 0.348 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	3.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11265385; hg19: chr1-160369819;