10-93881779-A-C

Variant names:

• chr10-93881779-A-C
• rs1477536
• ENST00000442978.1:n.160T>G

Variant summary

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

The ENST00000442978.1(RAB11AP1):​n.160T>G 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 0.903 in 540,694 control chromosomes in the GnomAD database, including 220,710 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 0.91 (62669 hom., cov: 34)
  • Exomes 𝑓: 0.90 (158041 hom.)
• Consequence: RAB11AP1 ENST00000442978.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 5 publications found

Genes affected

RAB11AP1 (HGNC:45188): (RAB11A, member RAS oncogene family pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442978.1. 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
	RAB11AP1	ENST00000442978.1	TSL:6	n.160T>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.907 AC: 137993 AN: 152166 Hom.: 62633 Cov.: 34

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.902

GnomAD4 exome AF: 0.901 AC: 349964 AN: 388410 Hom.: 158041 Cov.: 2 AF XY: 0.897 AC XY: 194647 AN XY: 217028

African (AFR) AF: 0.935 AC: 9691 AN: 10370

American (AMR) AF: 0.959 AC: 29205 AN: 30450

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 11029 AN: 11946

East Asian (EAS) AF: 0.892 AC: 16890 AN: 18934

South Asian (SAS) AF: 0.867 AC: 45816 AN: 52814

European-Finnish (FIN) AF: 0.951 AC: 29601 AN: 31116

Middle Eastern (MID) AF: 0.886 AC: 2675 AN: 3020

European-Non Finnish (NFE) AF: 0.891 AC: 187558 AN: 210386

Other (OTH) AF: 0.903 AC: 17499 AN: 19374

GnomAD4 genome AF: 0.907 AC: 138087 AN: 152284 Hom.: 62669 Cov.: 34 AF XY: 0.910 AC XY: 67716 AN XY: 74452

African (AFR) AF: 0.930 AC: 38654 AN: 41556

American (AMR) AF: 0.936 AC: 14318 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3193 AN: 3468

East Asian (EAS) AF: 0.884 AC: 4577 AN: 5180

South Asian (SAS) AF: 0.854 AC: 4119 AN: 4826

European-Finnish (FIN) AF: 0.954 AC: 10137 AN: 10624

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60097 AN: 68016

Other (OTH) AF: 0.902 AC: 1905 AN: 2112

Alfa AF: 0.896 Hom.: 68619

Bravo AF: 0.906

Asia WGS AF: 0.895 AC: 3116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1477536; hg19: chr10-95641536;