rs3935776

Positions:

• chr6-1515139-A-C
• chr6-1515139-A-G
• chr6-1515139-A-T

Variant summary

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

The ENST00000404600.2(ENSG00000218027):​n.151T>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 0.254 in 969,770 control chromosomes in the GnomAD database, including 33,008 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 0.29 (6791 hom., cov: 33)
  • Exomes 𝑓: 0.25 (26217 hom.)
• Consequence: ENST00000404600.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723944	XR_427861.4	n.235-12576T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000404600.2	n.151T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44745 AN: 151910 Hom.: 6788 Cov.: 33

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.302

GnomAD4 exome AF: 0.246 AC: 201181 AN: 817742 Hom.: 26217 Cov.: 12 AF XY: 0.250 AC XY: 107764 AN XY: 430560

Gnomad4 AFR exome AF: 0.326

Gnomad4 AMR exome AF: 0.242

Gnomad4 ASJ exome AF: 0.265

Gnomad4 EAS exome AF: 0.350

Gnomad4 SAS exome AF: 0.290

Gnomad4 FIN exome AF: 0.213

Gnomad4 NFE exome AF: 0.231

Gnomad4 OTH exome AF: 0.265

GnomAD4 genome AF: 0.295 AC: 44778 AN: 152028 Hom.: 6791 Cov.: 33 AF XY: 0.292 AC XY: 21731 AN XY: 74306

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.303

Alfa AF: 0.274 Hom.: 11725

Bravo AF: 0.304

Asia WGS AF: 0.346 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.8
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: rs3935776; hg19: chr6-1515374;