XM_047430819.1:c.729T>G

Variant names:

• chr13-33013514-A-C
• rs398655
• XM_047430819.1:c.729T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047430819.1(LOC124903151):​c.729T>G​(p.His243Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,000 control chromosomes in the GnomAD database, including 20,741 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 0.51 (20741 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LOC124903151 XM_047430819.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 15 publications found

Genes affected

LOC124903151 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903151	XM_047430819.1	c.729T>G	p.His243Gln	missense_variant	Exon 2 of 2		XP_047286775.1
LOC124903151	XR_007063749.1	n.339T>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308044	ENST00000830674.1	n.531T>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308044	ENST00000830675.1	n.694T>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308044	ENST00000830676.1	n.338T>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308044	ENST00000830677.1	n.266T>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77678 AN: 151884 Hom.: 20705 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.486

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.512 AC: 77756 AN: 152000 Hom.: 20741 Cov.: 32 AF XY: 0.516 AC XY: 38354 AN XY: 74290

African (AFR) AF: 0.642 AC: 26602 AN: 41458

American (AMR) AF: 0.627 AC: 9589 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1198 AN: 3472

East Asian (EAS) AF: 0.453 AC: 2342 AN: 5174

South Asian (SAS) AF: 0.414 AC: 1963 AN: 4744

European-Finnish (FIN) AF: 0.504 AC: 5327 AN: 10560

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29326 AN: 67996

Other (OTH) AF: 0.481 AC: 1014 AN: 2110

Alfa AF: 0.457 Hom.: 57550

Bravo AF: 0.530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.086
DANN	Benign	0.31
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs398655; hg19: chr13-33587652;