1-76018329-G-T

Position:

• chr1-76018329-G-T

Variant summary

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

The NR_125939.1(LOC101927342):​n.147-805G>T 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 0.411 in 151,936 control chromosomes in the GnomAD database, including 15,241 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 0.41 (15241 hom., cov: 31)
• Consequence: LOC101927342 NR_125939.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927342	NR_125939.1	n.147-805G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663316.1	n.682-805G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62405 AN: 151818 Hom.: 15242 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.411 AC: 62421 AN: 151936 Hom.: 15241 Cov.: 31 AF XY: 0.420 AC XY: 31171 AN XY: 74250

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.416

Alfa AF: 0.474 Hom.: 9421

Bravo AF: 0.389

Asia WGS AF: 0.659 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12753569; hg19: chr1-76484014;