rs11439060

Positions:

• chr4-87975555-T-TG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000662475.1(ENSG00000286618):​n.614_615insC 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 0.332 in 154,250 control chromosomes in the GnomAD database, including 8,831 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.33 (8756 hom., cov: 0)
  • Exomes 𝑓: 0.26 (75 hom.)
• Consequence: ENST00000662475.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662475.1	n.614_615insC		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50617 AN: 151820 Hom.: 8750 Cov.: 0

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.328

GnomAD4 exome AF: 0.258 AC: 598 AN: 2314 Hom.: 75 AF XY: 0.267 AC XY: 327 AN XY: 1224

Gnomad4 AFR exome AF: 0.300

Gnomad4 AMR exome AF: 0.261

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.241

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.289

Gnomad4 NFE exome AF: 0.254

Gnomad4 OTH exome AF: 0.279

GnomAD4 genome AF: 0.333 AC: 50650 AN: 151936 Hom.: 8756 Cov.: 0 AF XY: 0.334 AC XY: 24812 AN XY: 74262

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.328

Alfa AF: 0.308 Hom.: 621

Asia WGS AF: 0.295 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11439060; hg19: chr4-88896707;