rs308351

Variant names:

• chr11-67964485-G-A
• rs308351
• XM_047427952.1:c.339C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-67964485-G-A
• chr11-67964485-G-C
• chr11-67964485-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The XM_047427952.1(LOC112268076):​c.339C>T​(p.Asn113Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,964 control chromosomes in the GnomAD database, including 24,632 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 0.54 (24632 hom., cov: 31)
• Consequence: LOC112268076 XM_047427952.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 6 publications found

Genes affected

LOC112268076 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BP7: Synonymous conserved (PhyloP=-2.01 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81899 AN: 151846 Hom.: 24576 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.540 AC: 82014 AN: 151964 Hom.: 24632 Cov.: 31 AF XY: 0.530 AC XY: 39383 AN XY: 74268

African (AFR) AF: 0.829 AC: 34379 AN: 41488

American (AMR) AF: 0.412 AC: 6292 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1584 AN: 3468

East Asian (EAS) AF: 0.422 AC: 2160 AN: 5120

South Asian (SAS) AF: 0.423 AC: 2035 AN: 4812

European-Finnish (FIN) AF: 0.345 AC: 3634 AN: 10544

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30137 AN: 67946

Other (OTH) AF: 0.507 AC: 1068 AN: 2108

Alfa AF: 0.478 Hom.: 49563

Bravo AF: 0.553

Asia WGS AF: 0.462 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.28
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs308351; hg19: chr11-67731956;