chr22-42135691-T-C

Variant names:

• chr22-42135691-T-C
• rs9623531
• ENST00000621190.1:n.563T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000621190.1(NDUFA6-DT):​n.563T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.28 (2189 hom., cov: 6)
  • Failed GnomAD Quality Control
• Consequence: NDUFA6-DT ENST00000621190.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 5 publications found

Genes affected

NDUFA6-DT (HGNC:45273): (NDUFA6 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000621190.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDUFA6-DT	ENST00000621190.1	TSL:5	n.563T>C		non_coding_transcript_exon	Exon 5 of 8
	NDUFA6-DT	ENST00000439129.5	TSL:5	n.1719-508T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.280 AC: 12640 AN: 45134 Hom.: 2180 Cov.: 6

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.495

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.306

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.280 AC: 12658 AN: 45156 Hom.: 2189 Cov.: 6 AF XY: 0.282 AC XY: 5524 AN XY: 19606

African (AFR) AF: 0.295 AC: 2965 AN: 10044

American (AMR) AF: 0.295 AC: 1186 AN: 4022

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 447 AN: 1260

East Asian (EAS) AF: 0.106 AC: 307 AN: 2898

South Asian (SAS) AF: 0.340 AC: 432 AN: 1272

European-Finnish (FIN) AF: 0.338 AC: 840 AN: 2486

Middle Eastern (MID) AF: 0.488 AC: 83 AN: 170

European-Non Finnish (NFE) AF: 0.280 AC: 6157 AN: 22024

Other (OTH) AF: 0.303 AC: 187 AN: 618

Alfa AF: 0.338 Hom.: 1331

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.7
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs9623531; hg19: chr22-42531700;