rs1477536

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB11AP1		n.93881779A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB11AP1	ENST00000442978.1	n.160T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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;