rs6938239

Positions:

• chr6-34715858-G-A
• chr6-34715858-G-C

Variant summary

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

The ENST00000334441.4(ENSG00000186328):​n.246G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.845 in 170,734 control chromosomes in the GnomAD database, including 61,209 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 0.84 (53804 hom., cov: 30)
  • Exomes 𝑓: 0.89 (7405 hom.)
• Consequence: ENST00000334441.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.14

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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
	ENST00000334441.4	n.246G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127613 AN: 151924 Hom.: 53764 Cov.: 30

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.848

GnomAD4 exome AF: 0.888 AC: 16591 AN: 18692 Hom.: 7405 Cov.: 0 AF XY: 0.892 AC XY: 9293 AN XY: 10420

Gnomad4 AFR exome AF: 0.856

Gnomad4 AMR exome AF: 0.954

Gnomad4 ASJ exome AF: 0.896

Gnomad4 EAS exome AF: 0.992

Gnomad4 SAS exome AF: 0.946

Gnomad4 FIN exome AF: 0.813

Gnomad4 NFE exome AF: 0.896

Gnomad4 OTH exome AF: 0.898

GnomAD4 genome AF: 0.840 AC: 127711 AN: 152042 Hom.: 53804 Cov.: 30 AF XY: 0.839 AC XY: 62339 AN XY: 74318

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.849

Alfa AF: 0.831 Hom.: 7577

Bravo AF: 0.844

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6938239; hg19: chr6-34683635;