1-2569899-C-T

Variant names:

• chr1-2569899-C-T
• rs10797432
• NR_121638.1:n.71+3294C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_121638.1(LOC100996583):​n.71+3294C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,820 control chromosomes in the GnomAD database, including 20,478 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 (20475 hom., cov: 31)
  • Exomes 𝑓: 0.33 (3 hom.)
• Consequence: LOC100996583 NR_121638.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 52 publications found

Genes affected

LOC100996583 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_121638.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100996583	NR_121638.1		n.71+3294C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225931	ENST00000456687.3	TSL:5	n.*11C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78327 AN: 151662 Hom.: 20464 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.497

GnomAD4 exome AF: 0.325 AC: 13 AN: 40 Hom.: 3 Cov.: 0 AF XY: 0.333 AC XY: 8 AN XY: 24

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.306 AC: 11 AN: 36

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.516 AC: 78370 AN: 151780 Hom.: 20475 Cov.: 31 AF XY: 0.520 AC XY: 38559 AN XY: 74184

African (AFR) AF: 0.584 AC: 24151 AN: 41374

American (AMR) AF: 0.523 AC: 7982 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1558 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2774 AN: 5148

South Asian (SAS) AF: 0.658 AC: 3167 AN: 4814

European-Finnish (FIN) AF: 0.499 AC: 5256 AN: 10530

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32020 AN: 67878

Other (OTH) AF: 0.502 AC: 1053 AN: 2098

Alfa AF: 0.478 Hom.: 20804

Bravo AF: 0.513

Asia WGS AF: 0.659 AC: 2293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.72
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10797432; hg19: chr1-2501338;