rs1319730

Variant names:

• chr11-114027945-A-C
• rs1319730
• ENST00000770045.1:n.226-7317A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000770045.1(ENSG00000300211):​n.226-7317A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.947 in 152,290 control chromosomes in the GnomAD database, including 68,542 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 0.95 (68542 hom., cov: 33)
• Consequence: ENSG00000300211 ENST00000770045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 2 publications found

Genes affected

ENSG00000300211 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.978 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
ENSG00000300211	ENST00000770045.1	n.226-7317A>C		intron_variant	Intron 2 of 3
ENSG00000300211	ENST00000770046.1	n.141-7317A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.947 AC: 144168 AN: 152172 Hom.: 68506 Cov.: 33

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.993

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.947 AC: 144260 AN: 152290 Hom.: 68542 Cov.: 33 AF XY: 0.946 AC XY: 70462 AN XY: 74454

African (AFR) AF: 0.905 AC: 37596 AN: 41538

American (AMR) AF: 0.859 AC: 13142 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3455 AN: 3470

East Asian (EAS) AF: 0.877 AC: 4544 AN: 5182

South Asian (SAS) AF: 0.988 AC: 4763 AN: 4822

European-Finnish (FIN) AF: 0.993 AC: 10547 AN: 10618

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.985 AC: 66996 AN: 68042

Other (OTH) AF: 0.951 AC: 2013 AN: 2116

Alfa AF: 0.952 Hom.: 84997

Bravo AF: 0.931

Asia WGS AF: 0.915 AC: 3185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	18
DANN	Benign	0.76
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1319730; hg19: chr11-113898667;