chr1-192236902-A-G

Position:

• chr1-192236902-A-G

Variant summary

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

The XR_001738346.1(LOC105371662):​n.147-481T>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 0.523 in 151,912 control chromosomes in the GnomAD database, including 22,047 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 0.52 (22047 hom., cov: 32)
• Consequence: LOC105371662 XR_001738346.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

Genes affected

LOC105371662 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371662	XR_001738346.1	n.147-481T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000643151.1	n.412+1616T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79423 AN: 151794 Hom.: 22013 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.523 AC: 79496 AN: 151912 Hom.: 22047 Cov.: 32 AF XY: 0.520 AC XY: 38625 AN XY: 74216

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.495

Alfa AF: 0.466 Hom.: 21508

Bravo AF: 0.516

Asia WGS AF: 0.419 AC: 1457 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1175111; hg19: chr1-192206032;