4-102499861-A-G

Position:

• chr4-102499861-A-G

Variant summary

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

The NR_136202.1(LOC105377621):​n.48+2578T>C 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 0.125 in 151,960 control chromosomes in the GnomAD database, including 2,367 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 0.13 (2367 hom., cov: 31)
• Consequence: LOC105377621 NR_136202.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

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 = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377621	NR_136202.1	n.48+2578T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18971 AN: 151842 Hom.: 2360 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0625

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.0520

Gnomad SAS AF: 0.0409

Gnomad FIN AF: 0.0654

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0469

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.125 AC: 19002 AN: 151960 Hom.: 2367 Cov.: 31 AF XY: 0.123 AC XY: 9105 AN XY: 74268

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.0624

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.0516

Gnomad4 SAS AF: 0.0416

Gnomad4 FIN AF: 0.0654

Gnomad4 NFE AF: 0.0469

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0241 Hom.: 13

Bravo AF: 0.135

Asia WGS AF: 0.0660 AC: 229 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	4.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11944443; hg19: chr4-103421018;