rs11776207

Variant names:

• chr8-33907608-A-C
• rs11776207
• ENST00000521541.2:n.314-100248A>C

Variant summary

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

The ENST00000521541.2(ENSG00000253642):​n.314-100248A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,890 control chromosomes in the GnomAD database, including 15,808 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 0.45 (15808 hom., cov: 32)
• Consequence: ENSG00000253642 ENST00000521541.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 6 publications found

Genes affected

ENSG00000253642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521541.2. 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
	LOC105379364	NR_189605.1		n.745+111172A>C		intron	N/A
	LOC105379364	NR_189606.1		n.331-100248A>C		intron	N/A
	LOC105379364	NR_189607.1		n.330+111172A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253642	ENST00000521541.2	TSL:2	n.314-100248A>C		intron	N/A
	ENSG00000253642	ENST00000523063.5	TSL:3	n.505-100248A>C		intron	N/A
	ENSG00000253642	ENST00000523336.2	TSL:2	n.148-100248A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68142 AN: 151772 Hom.: 15791 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.449 AC: 68185 AN: 151890 Hom.: 15808 Cov.: 32 AF XY: 0.449 AC XY: 33348 AN XY: 74210

African (AFR) AF: 0.410 AC: 16972 AN: 41390

American (AMR) AF: 0.430 AC: 6560 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1123 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4098 AN: 5154

South Asian (SAS) AF: 0.624 AC: 3003 AN: 4810

European-Finnish (FIN) AF: 0.417 AC: 4400 AN: 10546

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.452 AC: 30676 AN: 67942

Other (OTH) AF: 0.437 AC: 923 AN: 2110

Alfa AF: 0.452 Hom.: 53190

Bravo AF: 0.446

Asia WGS AF: 0.680 AC: 2362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.70
PhyloP100		-0.64

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: rs11776207;

hg19: chr8-33765126;