rs11577354

Variant names:

• chr1-235103812-G-A
• rs11577354
• ENST00000812263.1:n.315+218C>T

Variant summary

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

The ENST00000812263.1(ENSG00000273416):​n.315+218C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 150,816 control chromosomes in the GnomAD database, including 21,437 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 0.53 (21437 hom., cov: 28)
• Consequence: ENSG00000273416 ENST00000812263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 6 publications found

Genes affected

ENSG00000273416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.575 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
ENSG00000273416	ENST00000812263.1	n.315+218C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.530 AC: 79929 AN: 150734 Hom.: 21424 Cov.: 28

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.530 AC: 79984 AN: 150816 Hom.: 21437 Cov.: 28 AF XY: 0.534 AC XY: 39258 AN XY: 73554

African (AFR) AF: 0.561 AC: 23003 AN: 41018

American (AMR) AF: 0.510 AC: 7708 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1619 AN: 3460

East Asian (EAS) AF: 0.389 AC: 1982 AN: 5100

South Asian (SAS) AF: 0.593 AC: 2844 AN: 4794

European-Finnish (FIN) AF: 0.590 AC: 6059 AN: 10270

Middle Eastern (MID) AF: 0.382 AC: 110 AN: 288

European-Non Finnish (NFE) AF: 0.519 AC: 35168 AN: 67788

Other (OTH) AF: 0.485 AC: 1010 AN: 2084

Alfa AF: 0.517 Hom.: 30938

Bravo AF: 0.520

Asia WGS AF: 0.486 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.73
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs11577354; hg19: chr1-235267127;