rs79271207

chr7-128913836-C-T

Variant summary

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

The ENST00000469533.1(ENSG00000224163):n.218+10G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 1,489,608 control chromosomes in the GnomAD database, including 22,954 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 0.20 (3712 hom., cov: 31)
  • Exomes 𝑓: 0.16 (19242 hom.)
• Consequence: ENST00000469533.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 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
	ENST00000469533.1	n.218+10G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30194 AN: 149630 Hom.: 3706 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0826

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.0983

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.156 AC: 208436 AN: 1339858 Hom.: 19242 Cov.: 22 AF XY: 0.158 AC XY: 106191 AN XY: 670872

Gnomad4 AFR exome AF: 0.268

Gnomad4 AMR exome AF: 0.162

Gnomad4 ASJ exome AF: 0.151

Gnomad4 EAS exome AF: 0.536

Gnomad4 SAS exome AF: 0.219

Gnomad4 FIN exome AF: 0.111

Gnomad4 NFE exome AF: 0.134

Gnomad4 OTH exome AF: 0.166

GnomAD4 genome AF: 0.202 AC: 30218 AN: 149750 Hom.: 3712 Cov.: 31 AF XY: 0.198 AC XY: 14467 AN XY: 73074

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.0983

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.184

Alfa AF: 0.185 Hom.: 313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.23
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2643764; hg19: chr7-128553890; COSMIC: COSV52823237;