rs11643723

Variant names:

• chr16-60427975-G-A
• rs11643723
• ENST00000565133.1:n.355-12588G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-60427975-G-A
• chr16-60427975-G-C

Variant summary

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

The ENST00000565133.1(ENSG00000261436):​n.355-12588G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 152,150 control chromosomes in the GnomAD database, including 483 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 0.073 (483 hom., cov: 32)
• Consequence: ENSG00000261436 ENST00000565133.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 2 publications found

Genes affected

ENSG00000261436 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565133.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261436	ENST00000565133.1	TSL:3	n.355-12588G>A		intron	N/A
	ENSG00000261436	ENST00000659433.2		n.299-44761G>A		intron	N/A
	ENSG00000261436	ENST00000660937.2		n.470-12588G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0726 AC: 11043 AN: 152032 Hom.: 484 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0446

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.00809

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0726 AC: 11050 AN: 152150 Hom.: 483 Cov.: 32 AF XY: 0.0717 AC XY: 5332 AN XY: 74392

African (AFR) AF: 0.122 AC: 5069 AN: 41498

American (AMR) AF: 0.0445 AC: 679 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0842 AC: 292 AN: 3468

East Asian (EAS) AF: 0.00792 AC: 41 AN: 5178

South Asian (SAS) AF: 0.0284 AC: 137 AN: 4824

European-Finnish (FIN) AF: 0.0763 AC: 807 AN: 10578

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.0561 AC: 3813 AN: 68016

Other (OTH) AF: 0.0776 AC: 164 AN: 2114

Alfa AF: 0.0638 Hom.: 529

Bravo AF: 0.0720

Asia WGS AF: 0.0330 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.42
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11643723;

hg19: chr16-60461879;