rs1080985

Variant names:

• chr22-42132375-G-C
• rs1080985
• ENST00000617009.4:n.166G>C

Your query was ambiguous. Multiple possible variants found:

• chr22-42132375-G-C
• chr22-42132375-G-A
• chr22-42132375-G-T

Variant summary

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

The ENST00000617009.4(NDUFA6-DT):​n.166G>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 0.194 in 150,524 control chromosomes in the GnomAD database, including 4,008 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as other (★).

• Frequency:
  • Genomes: 𝑓 0.19 (4004 hom., cov: 31)
  • Exomes 𝑓: 0.18 (4 hom.)
• Consequence: NDUFA6-DT ENST00000617009.4 non_coding_transcript_exon
• Clinical Significance: other criteria provided, single submitter O:1
• Conservation: PhyloP100: -0.693
• Publications: 126 publications found

Genes affected

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

ENSG00000227370 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000617009.4. 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
	NDUFA6-DT	ENST00000617009.4	TSL:5	n.166G>C		non_coding_transcript_exon	Exon 2 of 5
	NDUFA6-DT	ENST00000621190.1	TSL:5	n.166G>C		non_coding_transcript_exon	Exon 2 of 8
	NDUFA6-DT	ENST00000439129.5	TSL:5	n.1719-3824G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29130 AN: 150260 Hom.: 3998 Cov.: 31

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.221

GnomAD4 exome AF: 0.180 AC: 27 AN: 150 Hom.: 4 Cov.: 0 AF XY: 0.190 AC XY: 22 AN XY: 116

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 12

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.250 AC: 1 AN: 4

European-Non Finnish (NFE) AF: 0.205 AC: 25 AN: 122

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.194 AC: 29140 AN: 150374 Hom.: 4004 Cov.: 31 AF XY: 0.201 AC XY: 14756 AN XY: 73466

African (AFR) AF: 0.0770 AC: 3135 AN: 40726

American (AMR) AF: 0.227 AC: 3433 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3468

East Asian (EAS) AF: 0.115 AC: 585 AN: 5104

South Asian (SAS) AF: 0.253 AC: 1199 AN: 4744

European-Finnish (FIN) AF: 0.358 AC: 3743 AN: 10448

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15791 AN: 67466

Other (OTH) AF: 0.220 AC: 457 AN: 2082

Alfa AF: 0.128 Hom.: 306

Bravo AF: 0.178

ClinVar

ClinVar submissions

Significance: other

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
PhyloP100		-0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1080985;

hg19: chr22-42528382;