rs1491846

Variant names:

• chr11-27877467-A-G
• rs1491846
• ENST00000530663.1:n.147+35T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-27877467-A-G
• chr11-27877467-A-T

Variant summary

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

The ENST00000530663.1(ENSG00000255496):​n.147+35T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,184 control chromosomes in the GnomAD database, including 52,537 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 0.83 (52537 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 4 publications found

Genes affected

ENSG00000255496 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255496	ENST00000530663.1	n.147+35T>C		intron_variant	Intron 1 of 1	1
ENSG00000310355	ENST00000849264.1	n.223+683A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126045 AN: 152066 Hom.: 52511 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.850

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.829 AC: 126119 AN: 152184 Hom.: 52537 Cov.: 32 AF XY: 0.831 AC XY: 61822 AN XY: 74398

African (AFR) AF: 0.801 AC: 33266 AN: 41512

American (AMR) AF: 0.792 AC: 12094 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3025 AN: 3472

East Asian (EAS) AF: 0.682 AC: 3523 AN: 5164

South Asian (SAS) AF: 0.738 AC: 3559 AN: 4820

European-Finnish (FIN) AF: 0.938 AC: 9958 AN: 10612

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57885 AN: 68012

Other (OTH) AF: 0.850 AC: 1795 AN: 2112

Alfa AF: 0.847 Hom.: 7054

Bravo AF: 0.819

Asia WGS AF: 0.731 AC: 2543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.9
DANN	Benign	0.80
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs1491846; hg19: chr11-27899014;