rs13137776

Positions:

• chr4-11463351-A-G

Variant summary

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

The XR_001741361.2(LOC107986178):​n.172A>G 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 0.256 in 152,030 control chromosomes in the GnomAD database, including 6,263 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 0.26 (6263 hom., cov: 31)
• Consequence: LOC107986178 XR_001741361.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

Genes affected

LOC107986178 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986178	XR_001741361.2	n.172A>G		non_coding_transcript_exon_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662830.1	n.313-1050A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38947 AN: 151912 Hom.: 6252 Cov.: 31

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.256 AC: 38973 AN: 152030 Hom.: 6263 Cov.: 31 AF XY: 0.262 AC XY: 19494 AN XY: 74296

Gnomad4 AFR AF: 0.0653

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.265

Alfa AF: 0.315 Hom.: 12752

Bravo AF: 0.238

Asia WGS AF: 0.389 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13137776; hg19: chr4-11464975;