rs11006702

chr10-18737678-C-T

Variant summary

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

The ENST00000413342.1(AIFM1P1):n.888C>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 0.251 in 339,510 control chromosomes in the GnomAD database, including 11,740 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 0.29 (6883 hom., cov: 32)
  • Exomes 𝑓: 0.22 (4857 hom.)
• Consequence: AIFM1P1 ENST00000413342.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.245

Genes affected

AIFM1P1 (HGNC:44884): (AIFM1 pseudogene 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376440	XR_930721.2	n.69-9011C>T		intron_variant, non_coding_transcript_variant
LOC105376440	XR_930720.2	n.51+27317C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AIFM1P1	ENST00000413342.1	n.888C>T		non_coding_transcript_exon_variant	2/2
	ENST00000654305.1	n.94-9011C>T		intron_variant, non_coding_transcript_variant
	ENST00000654415.1	n.109+5232C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43474 AN: 151764 Hom.: 6866 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.222 AC: 41564 AN: 187630 Hom.: 4857 Cov.: 0 AF XY: 0.218 AC XY: 23664 AN XY: 108618

Gnomad4 AFR exome AF: 0.416

Gnomad4 AMR exome AF: 0.174

Gnomad4 ASJ exome AF: 0.169

Gnomad4 EAS exome AF: 0.126

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.220

Gnomad4 NFE exome AF: 0.244

Gnomad4 OTH exome AF: 0.236

GnomAD4 genome AF: 0.287 AC: 43526 AN: 151880 Hom.: 6883 Cov.: 32 AF XY: 0.282 AC XY: 20946 AN XY: 74254

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.249

Alfa AF: 0.263 Hom.: 966

Bravo AF: 0.294

Asia WGS AF: 0.168 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	5.3
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11006702; hg19: chr10-19026607;