rs11136221

Variant names:

• chr8-46620127-A-C
• rs11136221
• ENST00000641977.1:n.552+18208T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-46620127-A-C
• chr8-46620127-A-T

Variant summary

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

The ENST00000641977.1(ENSG00000290398):​n.552+18208T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,988 control chromosomes in the GnomAD database, including 21,652 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 0.48 (21652 hom., cov: 33)
• Consequence: ENSG00000290398 ENST00000641977.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 2 publications found

Genes affected

ENSG00000290398 (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 = 0.658 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641977.1. 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
	ENSG00000290398	ENST00000641977.1		n.552+18208T>G		intron	N/A
	ENSG00000302462	ENST00000787002.1		n.132+2566A>C		intron	N/A
	ENSG00000302462	ENST00000787006.1		n.126+2566A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73170 AN: 151870 Hom.: 21653 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.481 AC: 73156 AN: 151988 Hom.: 21652 Cov.: 33 AF XY: 0.478 AC XY: 35484 AN XY: 74290

African (AFR) AF: 0.125 AC: 5193 AN: 41428

American (AMR) AF: 0.535 AC: 8170 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1893 AN: 3472

East Asian (EAS) AF: 0.561 AC: 2886 AN: 5140

South Asian (SAS) AF: 0.383 AC: 1850 AN: 4824

European-Finnish (FIN) AF: 0.595 AC: 6292 AN: 10572

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45055 AN: 67970

Other (OTH) AF: 0.501 AC: 1060 AN: 2114

Alfa AF: 0.565 Hom.: 11467

Bravo AF: 0.461

Asia WGS AF: 0.403 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs11136221; hg19: chr8-47531749;