rs72639219

Positions:

• chr3-49029512-G-A

Variant summary

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

The ENST00000607245.1(ENSG00000272434):​n.197G>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 0.00512 in 697,674 control chromosomes in the GnomAD database, including 92 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 0.016 (64 hom., cov: 33)
  • Exomes 𝑓: 0.0021 (28 hom.)
• Consequence: ENST00000607245.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000607245.1	n.197G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0159 AC: 2420 AN: 152242 Hom.: 62 Cov.: 33

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0100

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.0105

GnomAD3 exomes AF: 0.00369 AC: 465 AN: 125852 Hom.: 13 AF XY: 0.00308 AC XY: 213 AN XY: 69058

Gnomad AFR exome AF: 0.0589

Gnomad AMR exome AF: 0.00386

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000196

Gnomad SAS exome AF: 0.0000453

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000837

Gnomad OTH exome AF: 0.00103

GnomAD4 exome AF: 0.00209 AC: 1141 AN: 545314 Hom.: 28 Cov.: 5 AF XY: 0.00175 AC XY: 515 AN XY: 294814

Gnomad4 AFR exome AF: 0.0550

Gnomad4 AMR exome AF: 0.00394

Gnomad4 ASJ exome AF: 0.0000508

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000977

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000537

Gnomad4 OTH exome AF: 0.00421

GnomAD4 genome AF: 0.0159 AC: 2428 AN: 152360 Hom.: 64 Cov.: 33 AF XY: 0.0154 AC XY: 1144 AN XY: 74498

Gnomad4 AFR AF: 0.0539

Gnomad4 AMR AF: 0.00999

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000588

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.00630 Hom.: 7

Bravo AF: 0.0185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.1
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72639219; hg19: chr3-49066945;