6-122438270-T-C

Variant names:

• chr6-122438270-T-C
• rs577838
• ENST00000624649.1:n.954A>G

Variant summary

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

The ENST00000624649.1(ENSG00000279453):​n.954A>G 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 0.797 in 152,062 control chromosomes in the GnomAD database, including 48,486 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 0.80 (48471 hom., cov: 31)
  • Exomes 𝑓: 0.84 (15 hom.)
• Consequence: ENSG00000279453 ENST00000624649.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

Genes affected

ENSG00000279453 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.897 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
ENSG00000279453	ENST00000624649.1	n.954A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121010 AN: 151900 Hom.: 48431 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.800

GnomAD4 exome AF: 0.841 AC: 37 AN: 44 Hom.: 15 Cov.: 0 AF XY: 0.833 AC XY: 30 AN XY: 36

Gnomad4 AMR exome AF: 0.500

Gnomad4 NFE exome AF: 0.875

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.797 AC: 121107 AN: 152018 Hom.: 48471 Cov.: 31 AF XY: 0.797 AC XY: 59209 AN XY: 74280

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.802

Alfa AF: 0.817 Hom.: 78334

Bravo AF: 0.800

Asia WGS AF: 0.860 AC: 2993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs577838; hg19: chr6-122759415;