rs198820

Positions:

• chr6-26124015-G-A

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.843G>A 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 0.347 in 1,450,462 control chromosomes in the GnomAD database, including 90,987 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 (7334 hom., cov: 32)
  • Exomes 𝑓: 0.35 (83653 hom.)
• Consequence: ENST00000707189.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 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
	ENST00000707189.1	n.843G>A		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43699 AN: 151948 Hom.: 7332 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.255

GnomAD4 exome AF: 0.353 AC: 458968 AN: 1298396 Hom.: 83653 Cov.: 21 AF XY: 0.354 AC XY: 227499 AN XY: 643120

Gnomad4 AFR exome AF: 0.104

Gnomad4 AMR exome AF: 0.329

Gnomad4 ASJ exome AF: 0.294

Gnomad4 EAS exome AF: 0.108

Gnomad4 SAS exome AF: 0.336

Gnomad4 FIN exome AF: 0.367

Gnomad4 NFE exome AF: 0.374

Gnomad4 OTH exome AF: 0.336

GnomAD4 genome AF: 0.287 AC: 43719 AN: 152066 Hom.: 7334 Cov.: 32 AF XY: 0.286 AC XY: 21254 AN XY: 74328

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.258

Alfa AF: 0.311 Hom.: 761

Bravo AF: 0.274

Asia WGS AF: 0.270 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	1.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs198820; hg19: chr6-26124243; COSMIC: COSV58415959;