rs230487

Positions:

• chr4-102468252-C-A

Variant summary

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

The NR_136202.1(LOC105377621):​n.49-18185G>T 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 0.715 in 152,028 control chromosomes in the GnomAD database, including 39,411 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 0.71 (39411 hom., cov: 31)
• Consequence: LOC105377621 NR_136202.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889

Genes affected

LOC105377621 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377621	NR_136202.1	n.49-18185G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108506 AN: 151908 Hom.: 39346 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.715 AC: 108628 AN: 152028 Hom.: 39411 Cov.: 31 AF XY: 0.714 AC XY: 53048 AN XY: 74306

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.672

Alfa AF: 0.697 Hom.: 49517

Bravo AF: 0.712

Asia WGS AF: 0.434 AC: 1506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230487; hg19: chr4-103389409;