rs11006702

Variant names:

• chr10-18737678-C-T
• rs11006702
• ENST00000413342.1:n.888C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ENSG00000234244 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413342.1. 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
	AIFM1P1	ENST00000413342.1	TSL:6	n.888C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000234244	ENST00000654305.2		n.104-9011C>T		intron	N/A
	ENSG00000234244	ENST00000654415.1		n.109+5232C>T		intron	N/A

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

African (AFR) AF: 0.416 AC: 1538 AN: 3700

American (AMR) AF: 0.174 AC: 2296 AN: 13166

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 625 AN: 3690

East Asian (EAS) AF: 0.126 AC: 802 AN: 6358

South Asian (SAS) AF: 0.167 AC: 5214 AN: 31178

European-Finnish (FIN) AF: 0.220 AC: 2433 AN: 11082

Middle Eastern (MID) AF: 0.143 AC: 307 AN: 2154

European-Non Finnish (NFE) AF: 0.244 AC: 26250 AN: 107422

Other (OTH) AF: 0.236 AC: 2099 AN: 8880

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

African (AFR) AF: 0.420 AC: 17367 AN: 41364

American (AMR) AF: 0.242 AC: 3698 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3470

East Asian (EAS) AF: 0.136 AC: 703 AN: 5166

South Asian (SAS) AF: 0.183 AC: 879 AN: 4800

European-Finnish (FIN) AF: 0.225 AC: 2376 AN: 10558

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16873 AN: 67962

Other (OTH) AF: 0.249 AC: 524 AN: 2108

Alfa AF: 0.267 Hom.: 1024

Bravo AF: 0.294

Asia WGS AF: 0.168 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	5.3
DANN	Benign	0.55
PhyloP100		0.24

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: rs11006702;

hg19: chr10-19026607;