4-102497800-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.48+4639A>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 0.423 in 151,976 control chromosomes in the GnomAD database, including 13,827 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 0.42 (13827 hom., cov: 31)
• Consequence: LOC105377621 NR_136202.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.676

Genes affected

LOC105377621 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377621	NR_136202.1	n.48+4639A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64147 AN: 151858 Hom.: 13803 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.423 AC: 64213 AN: 151976 Hom.: 13827 Cov.: 31 AF XY: 0.423 AC XY: 31424 AN XY: 74278

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.394

Alfa AF: 0.410 Hom.: 2164

Bravo AF: 0.432

Asia WGS AF: 0.351 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.5
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: rs980455; hg19: chr4-103418957;