ENST00000624264.1:n.6306A>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000279217 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624264.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000279217	ENST00000624264.1	TSL:6	n.6306A>C		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.167 AC: 3 AN: 18

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.590 AC: 24441 AN: 41454

American (AMR) AF: 0.208 AC: 3178 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 715 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1222 AN: 5166

South Asian (SAS) AF: 0.196 AC: 944 AN: 4814

European-Finnish (FIN) AF: 0.236 AC: 2498 AN: 10590

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15220 AN: 67970

Other (OTH) AF: 0.285 AC: 603 AN: 2114

Alfa AF: 0.251 Hom.: 6829

Bravo AF: 0.335

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.48
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs715550; hg19: chr22-36473353;