rs11049998

Variant names:

• chr12-29041512-T-C
• rs11049998
• XR_001749059.1:n.337T>C

Variant summary

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

The XR_242930.3(LOC101928735):​n.337T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,516 control chromosomes in the GnomAD database, including 2,098 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 0.16 (2098 hom., cov: 30)
• Consequence: LOC101928735 XR_242930.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.64

Genes affected

LOC101928735 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928735	XR_001749059.1	n.337T>C		non_coding_transcript_exon_variant	Exon 2 of 7
LOC101928735	XR_242930.3	n.337T>C		non_coding_transcript_exon_variant	Exon 2 of 5
LOC101928735	XR_931469.2	n.337T>C		non_coding_transcript_exon_variant	Exon 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24472 AN: 151398 Hom.: 2095 Cov.: 30

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.162 AC: 24486 AN: 151516 Hom.: 2098 Cov.: 30 AF XY: 0.157 AC XY: 11641 AN XY: 73980

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.157

Alfa AF: 0.169 Hom.: 1193

Bravo AF: 0.161

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11049998; hg19: chr12-29194445;