rs1481964

Variant names:

• chr11-103523111-G-A
• rs1481964
• ENST00000827359.1:n.219-3884C>T

Variant summary

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

The ENST00000827359.1(ENSG00000307600):​n.219-3884C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,908 control chromosomes in the GnomAD database, including 13,713 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 0.40 (13713 hom., cov: 31)
• Consequence: ENSG00000307600 ENST00000827359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 1 publications found

Genes affected

ENSG00000307600 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 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
ENSG00000307600	ENST00000827359.1	n.219-3884C>T		intron_variant	Intron 2 of 2
ENSG00000307600	ENST00000827360.1	n.93-3884C>T		intron_variant	Intron 1 of 1
ENSG00000307600	ENST00000827361.1	n.106-3884C>T		intron_variant	Intron 1 of 1
ENSG00000307600	ENST00000827362.1	n.227+3850C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60447 AN: 151792 Hom.: 13715 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.417

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.398 AC: 60450 AN: 151908 Hom.: 13713 Cov.: 31 AF XY: 0.393 AC XY: 29153 AN XY: 74250

African (AFR) AF: 0.194 AC: 8016 AN: 41420

American (AMR) AF: 0.365 AC: 5565 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3468

East Asian (EAS) AF: 0.221 AC: 1137 AN: 5154

South Asian (SAS) AF: 0.354 AC: 1703 AN: 4814

European-Finnish (FIN) AF: 0.482 AC: 5077 AN: 10538

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35826 AN: 67948

Other (OTH) AF: 0.413 AC: 872 AN: 2112

Alfa AF: 0.420 Hom.: 2376

Bravo AF: 0.381

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1481964; hg19: chr11-103393839;