rs308351

Positions:

• chr11-67964485-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The XM_047427952.1(LOC112268076):​c.339C>T​(p.Asn113=) 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

Genes affected

LOC112268076 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268076	XM_047427952.1	c.339C>T	p.Asn113=	synonymous_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.507

Alfa AF: 0.455 Hom.: 25696

Bravo AF: 0.553

Asia WGS AF: 0.462 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs308351; hg19: chr11-67731956;