4-138247487-A-T

Position:

• chr4-138247487-A-T

Variant summary

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

The XM_047449956.1(SLC7A11):​c.51-5426T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,542 control chromosomes in the GnomAD database, including 13,099 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 0.40 (13099 hom., cov: 31)
• Consequence: SLC7A11 XM_047449956.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

Genes affected

SLC7A11 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC7A11	XM_047449956.1	c.51-5426T>A		intron_variant
SLC7A11	XM_047449957.1	c.51-5426T>A		intron_variant
SLC7A11	XM_047449958.1	c.51-5426T>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60906 AN: 151424 Hom.: 13092 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.402 AC: 60935 AN: 151542 Hom.: 13099 Cov.: 31 AF XY: 0.399 AC XY: 29542 AN XY: 74052

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.410

Alfa AF: 0.433 Hom.: 1852

Bravo AF: 0.390

Asia WGS AF: 0.418 AC: 1438 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.66
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: rs6841268; hg19: chr4-139168641;