chr1-103477009-T-C

Position:

• chr1-103477009-T-C

Variant summary

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

The NR_168321.1(RNPC3-DT):​n.114-43913A>G 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 0.114 in 152,000 control chromosomes in the GnomAD database, including 1,084 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 0.11 (1084 hom., cov: 32)
• Consequence: RNPC3-DT NR_168321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

RNPC3-DT (HGNC:55855): (RNPC3 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNPC3-DT	NR_168321.1	n.114-43913A>G		intron_variant, non_coding_transcript_variant
RNPC3-DT	NR_168319.1	n.114-7619A>G		intron_variant, non_coding_transcript_variant
RNPC3-DT	NR_168320.1	n.114-43913A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNPC3-DT	ENST00000662345.1	n.110-43913A>G		intron_variant, non_coding_transcript_variant
RNPC3-DT	ENST00000444810.6	n.117-7619A>G		intron_variant, non_coding_transcript_variant		3
RNPC3-DT	ENST00000447322.3	n.114-7619A>G		intron_variant, non_coding_transcript_variant		3
RNPC3-DT	ENST00000668150.1	n.114-43913A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17310 AN: 151882 Hom.: 1080 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0897

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.114 AC: 17336 AN: 152000 Hom.: 1084 Cov.: 32 AF XY: 0.113 AC XY: 8413 AN XY: 74292

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0897

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.0929

Gnomad4 FIN AF: 0.0767

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.111

Alfa AF: 0.102 Hom.: 1182

Bravo AF: 0.118

Asia WGS AF: 0.133 AC: 461 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7524694; hg19: chr1-104019631;