chr1-56385014-C-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

ENSG00000284686 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.313 AC: 12958 AN: 41452

American (AMR) AF: 0.0993 AC: 1518 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3470

East Asian (EAS) AF: 0.0934 AC: 483 AN: 5174

South Asian (SAS) AF: 0.0740 AC: 357 AN: 4826

European-Finnish (FIN) AF: 0.0995 AC: 1053 AN: 10582

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7264 AN: 67992

Other (OTH) AF: 0.132 AC: 278 AN: 2114

Alfa AF: 0.113 Hom.: 3513

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
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs11206801; hg19: chr1-56850686;