1-224212938-C-G

Position:

• chr1-224212938-C-G

Variant summary

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

The NR_110669.1(LOC101927143):​n.342G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,120 control chromosomes in the GnomAD database, including 50,107 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 0.81 (50090 hom., cov: 30)
  • Exomes 𝑓: 0.79 (17 hom.)
• Consequence: LOC101927143 NR_110669.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927143	NR_110669.1	n.342G>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000436706.1	n.342G>C		non_coding_transcript_exon_variant	1/2	1
	ENST00000664126.1	n.688G>C		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122777 AN: 151950 Hom.: 50081 Cov.: 30

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.792

GnomAD4 exome AF: 0.788 AC: 41 AN: 52 Hom.: 17 Cov.: 0 AF XY: 0.750 AC XY: 30 AN XY: 40

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.804

GnomAD4 genome AF: 0.808 AC: 122837 AN: 152068 Hom.: 50090 Cov.: 30 AF XY: 0.811 AC XY: 60305 AN XY: 74344

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.793

Alfa AF: 0.805 Hom.: 2480

Bravo AF: 0.787

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.78
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4290029; hg19: chr1-224400640;