rs1519337

Positions:

• chr4-138011920-G-A
• chr4-138011920-G-C
• chr4-138011920-G-T

Variant summary

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

The variant allele was found at a frequency of 0.889 in 152,216 control chromosomes in the GnomAD database, including 60,366 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 0.89 (60366 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.138011920G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287144	ENST00000655176.1	n.661-13314G>A		intron_variant
LINC00616	ENST00000656980.1	n.844-33155C>T		intron_variant
LINC00616	ENST00000661963.1	n.806-33155C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135162 AN: 152098 Hom.: 60324 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.889 AC: 135265 AN: 152216 Hom.: 60366 Cov.: 32 AF XY: 0.890 AC XY: 66224 AN XY: 74438

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.964

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.964

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.907

Alfa AF: 0.912 Hom.: 37506

Bravo AF: 0.876

Asia WGS AF: 0.910 AC: 3157 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.8
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1519337; hg19: chr4-138933074;