rs11161841

Variant names:

• chr1-86537789-T-A
• rs11161841

Variant summary

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

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 0.028 (223 hom., cov: 16)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0821 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0276 AC: 2975 AN: 107912 Hom.: 223 Cov.: 16

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.00971

Gnomad AMR AF: 0.0123

Gnomad ASJ AF: 0.00556

Gnomad EAS AF: 0.00415

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.0117

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00916

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0276 AC: 2977 AN: 107886 Hom.: 223 Cov.: 16 AF XY: 0.0276 AC XY: 1417 AN XY: 51304

African (AFR) AF: 0.0850 AC: 2176 AN: 25588

American (AMR) AF: 0.0122 AC: 132 AN: 10814

Ashkenazi Jewish (ASJ) AF: 0.00556 AC: 15 AN: 2698

East Asian (EAS) AF: 0.00417 AC: 17 AN: 4080

South Asian (SAS) AF: 0.0126 AC: 42 AN: 3344

European-Finnish (FIN) AF: 0.0117 AC: 61 AN: 5206

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 152

European-Non Finnish (NFE) AF: 0.00916 AC: 494 AN: 53928

Other (OTH) AF: 0.0233 AC: 34 AN: 1458

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.22
PhyloP100		0.39

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: rs11161841;

hg19: chr1-87003472;

COSMIC: COSV59968424;