rs3803239

chr13-109787607-C-G

Variant summary

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

The XM_047430835.1(LOC124903211):c.361C>G(p.Leu121Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 151,384 control chromosomes in the GnomAD database, including 1,201 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict 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 (1201 hom., cov: 31)
• Consequence: LOC124903211 XM_047430835.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471

Genes affected

LOC124903211 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903211	XM_047430835.1	c.361C>G	p.Leu121Val	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000615635.1	n.115+1662C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16890 AN: 151264 Hom.: 1201 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.0309

Gnomad EAS AF: 0.0430

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.0979

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.112 AC: 16919 AN: 151384 Hom.: 1201 Cov.: 31 AF XY: 0.111 AC XY: 8202 AN XY: 73944

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0875

Gnomad4 ASJ AF: 0.0309

Gnomad4 EAS AF: 0.0433

Gnomad4 SAS AF: 0.0565

Gnomad4 FIN AF: 0.0979

Gnomad4 NFE AF: 0.0793

Gnomad4 OTH AF: 0.100

Alfa AF: 0.101 Hom.: 142

Bravo AF: 0.117

Asia WGS AF: 0.0530 AC: 183 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	6.8
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3803239; hg19: chr13-110439954;