rs715550

chr22-36077305-A-Cchr22-36077305-A-T

Variant summary

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

The ENST00000624264.1(ENSG00000279217):n.6306A>C 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 0.323 in 152,068 control chromosomes in the GnomAD database, including 10,002 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 0.32 (10001 hom., cov: 32)
  • Exomes 𝑓: 0.21 (1 hom.)
• Consequence: ENST00000624264.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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
	ENST00000624264.1	n.6306A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48976 AN: 151924 Hom.: 9975 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.284

GnomAD4 exome AF: 0.208 AC: 5 AN: 24 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 4 AN XY: 16

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.323 AC: 49059 AN: 152044 Hom.: 10001 Cov.: 32 AF XY: 0.319 AC XY: 23716 AN XY: 74312

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.285

Alfa AF: 0.237 Hom.: 4392

Bravo AF: 0.335

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.29
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs715550; hg19: chr22-36473353;