1-2571341-C-T

Position:

• chr1-2571341-C-T

Variant summary

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

The NR_121638.1(LOC100996583):​n.71+4736C>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 0.531 in 152,052 control chromosomes in the GnomAD database, including 21,657 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 0.53 (21657 hom., cov: 33)
• Consequence: LOC100996583 NR_121638.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755

Genes affected

LOC100996583 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100996583	NR_121638.1	n.71+4736C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80764 AN: 151934 Hom.: 21645 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.531 AC: 80809 AN: 152052 Hom.: 21657 Cov.: 33 AF XY: 0.536 AC XY: 39811 AN XY: 74326

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.516

Alfa AF: 0.497 Hom.: 28205

Bravo AF: 0.527

Asia WGS AF: 0.666 AC: 2317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6667605; hg19: chr1-2502780;