rs11206801

Variant names:

• chr1-56385014-C-A
• rs11206801
• ENST00000642129.1:n.*95+98249G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-56385014-C-A
• chr1-56385014-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642129.1(ENSG00000284686):​n.*95+98249G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,106 control chromosomes in the GnomAD database, including 2,617 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 0.16 (2617 hom., cov: 32)
• Consequence: ENSG00000284686 ENST00000642129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

Genes affected

ENSG00000284686 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 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
ENSG00000284686	ENST00000642129.1	n.*95+98249G>T		intron_variant	Intron 5 of 5			ENSP00000492927.1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24275 AN: 151988 Hom.: 2612 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0995

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.0927

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.0995

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.160 AC: 24316 AN: 152106 Hom.: 2617 Cov.: 32 AF XY: 0.157 AC XY: 11705 AN XY: 74364

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.0993

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.0934

Gnomad4 SAS AF: 0.0740

Gnomad4 FIN AF: 0.0995

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.132

Alfa AF: 0.107 Hom.: 2071

Bravo AF: 0.167

Asia WGS AF: 0.104 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11206801; hg19: chr1-56850686;