1-2567423-G-C

Position:

• chr1-2567423-G-C

Variant summary

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

The NR_121638.1(LOC100996583):​n.71+818G>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 0.531 in 152,114 control chromosomes in the GnomAD database, including 21,660 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 (21660 hom., cov: 33)
• Consequence: LOC100996583 NR_121638.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100996583	NR_121638.1	n.71+818G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000456687.3	n.197-443G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80787 AN: 151996 Hom.: 21649 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.662

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: 80831 AN: 152114 Hom.: 21660 Cov.: 33 AF XY: 0.535 AC XY: 39809 AN XY: 74344

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.516

Alfa AF: 0.351 Hom.: 863

Bravo AF: 0.527

Asia WGS AF: 0.665 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
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: rs1555791; hg19: chr1-2498862;