rs3803239

Variant names:

• chr13-109787607-C-G
• rs3803239
• XM_047430835.1:c.361C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

LOC124903211 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772577.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300524	ENST00000772577.1		n.77C>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000275741	ENST00000615635.1	TSL:4	n.115+1662C>G		intron	N/A
	ENSG00000275741	ENST00000772402.1		n.67+1662C>G		intron	N/A

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

African (AFR) AF: 0.200 AC: 8249 AN: 41204

American (AMR) AF: 0.0875 AC: 1334 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0309 AC: 107 AN: 3468

East Asian (EAS) AF: 0.0433 AC: 220 AN: 5082

South Asian (SAS) AF: 0.0565 AC: 270 AN: 4782

European-Finnish (FIN) AF: 0.0979 AC: 1034 AN: 10566

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0793 AC: 5371 AN: 67726

Other (OTH) AF: 0.100 AC: 211 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.8
DANN	Benign	0.65
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs3803239; hg19: chr13-110439954;