chr22-36077305-A-C

Variant names:

• chr22-36077305-A-C
• rs715550
• ENST00000624264.1:n.6306A>C

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: ENSG00000279217 ENST00000624264.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

Genes affected

ENSG00000279217 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279217	ENST00000624264.1	n.6306A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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;