rs11799391

Variant names:

• chr1-238136872-A-C
• rs11799391
• ENST00000780747.1:n.360+20208A>C

Variant summary

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

The ENST00000780747.1(ENSG00000301680):​n.360+20208A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0473 in 152,316 control chromosomes in the GnomAD database, including 200 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 0.047 (200 hom., cov: 32)
• Consequence: ENSG00000301680 ENST00000780747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 1 publications found

Genes affected

ENSG00000301680 (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 (SAS) allele frequency at 95% confidence interval = 0.094 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
ENSG00000301680	ENST00000780747.1	n.360+20208A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7190 AN: 152198 Hom.: 200 Cov.: 32

Gnomad AFR AF: 0.0559

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0318

Gnomad ASJ AF: 0.0892

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0473 AC: 7201 AN: 152316 Hom.: 200 Cov.: 32 AF XY: 0.0469 AC XY: 3492 AN XY: 74484

African (AFR) AF: 0.0562 AC: 2338 AN: 41574

American (AMR) AF: 0.0318 AC: 486 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0892 AC: 309 AN: 3464

East Asian (EAS) AF: 0.0359 AC: 186 AN: 5178

South Asian (SAS) AF: 0.101 AC: 489 AN: 4822

European-Finnish (FIN) AF: 0.0305 AC: 324 AN: 10624

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0433 AC: 2943 AN: 68034

Other (OTH) AF: 0.0511 AC: 108 AN: 2112

Alfa AF: 0.0461 Hom.: 19

Bravo AF: 0.0457

Asia WGS AF: 0.0930 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.77
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs11799391; hg19: chr1-238300172; COSMIC: COSV60041971;