rs230489

Positions:

• chr4-102467284-T-C

Variant summary

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

The NR_136202.1(LOC105377621):​n.49-17217A>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 0.105 in 152,256 control chromosomes in the GnomAD database, including 911 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 (911 hom., cov: 32)
• Consequence: LOC105377621 NR_136202.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

Genes affected

LOC105377621 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377621	NR_136202.1	n.49-17217A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16040 AN: 152138 Hom.: 910 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0896

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.105 AC: 16057 AN: 152256 Hom.: 911 Cov.: 32 AF XY: 0.105 AC XY: 7783 AN XY: 74458

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0449

Gnomad4 FIN AF: 0.0896

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.114

Alfa AF: 0.115 Hom.: 1396

Bravo AF: 0.109

Asia WGS AF: 0.0370 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230489; hg19: chr4-103388441;