chr8-132702241-G-A

Variant names:

• chr8-132702241-G-A
• rs3843561
• XR_007060728.1:n.667C>T

Variant summary

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

The XR_007060728.1(DNAAF11):​n.667C>T 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 0.183 in 152,070 control chromosomes in the GnomAD database, including 3,302 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 0.18 (3302 hom., cov: 32)
  • Exomes 𝑓: 0.14 (0 hom.)
• Consequence: DNAAF11 XR_007060728.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813
• Publications: 6 publications found

Genes affected

DNAAF11 (HGNC:16725): (dynein axonemal assembly factor 11) The protein encoded by this gene contains several leucine-rich repeat domains and appears to be involved in the motility of cilia. Defects in this gene are a cause of primary ciliary dyskinesia-19 (CILD19). Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 4, 11 and 22. [provided by RefSeq, Apr 2016]

TMEM71 (HGNC:26572): (transmembrane protein 71) Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522780.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM71	ENST00000522780.5	TSL:4	c.264-14586C>T		intron	N/A	ENSP00000428772.1
	TMEM71	ENST00000524079.5	TSL:2	n.-2C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27795 AN: 151930 Hom.: 3303 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.203

GnomAD4 exome AF: 0.136 AC: 3 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10

African (AFR) AF: 0.00 AC: 0 AN: 2

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: 0.143 AC: 2 AN: 14

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

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

GnomAD4 genome AF: 0.183 AC: 27793 AN: 152048 Hom.: 3302 Cov.: 32 AF XY: 0.189 AC XY: 14078 AN XY: 74294

African (AFR) AF: 0.0448 AC: 1862 AN: 41518

American (AMR) AF: 0.298 AC: 4556 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3470

East Asian (EAS) AF: 0.314 AC: 1621 AN: 5162

South Asian (SAS) AF: 0.308 AC: 1483 AN: 4812

European-Finnish (FIN) AF: 0.242 AC: 2549 AN: 10532

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14419 AN: 67970

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.207 Hom.: 5778

Bravo AF: 0.178

Asia WGS AF: 0.290 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.64
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs3843561; hg19: chr8-133714487;