rs11206377

Variant names:

• chr1-39583432-A-G
• rs11206377
• ENST00000721383.1:n.380-6260A>G

Variant summary

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

The ENST00000721383.1(ENSG00000294134):​n.380-6260A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,058 control chromosomes in the GnomAD database, including 20,055 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 0.50 (20055 hom., cov: 28)
• Consequence: ENSG00000294134 ENST00000721383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 16 publications found

Genes affected

ENSG00000294134 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.757 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
ENSG00000294134	ENST00000721383.1	n.380-6260A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75497 AN: 150940 Hom.: 20055 Cov.: 28

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.500 AC: 75509 AN: 151058 Hom.: 20055 Cov.: 28 AF XY: 0.506 AC XY: 37322 AN XY: 73742

African (AFR) AF: 0.317 AC: 13039 AN: 41134

American (AMR) AF: 0.588 AC: 8935 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2063 AN: 3458

East Asian (EAS) AF: 0.538 AC: 2754 AN: 5116

South Asian (SAS) AF: 0.778 AC: 3703 AN: 4762

European-Finnish (FIN) AF: 0.536 AC: 5532 AN: 10316

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37730 AN: 67782

Other (OTH) AF: 0.501 AC: 1048 AN: 2090

Alfa AF: 0.539 Hom.: 9697

Bravo AF: 0.488

Asia WGS AF: 0.597 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.45
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs11206377; hg19: chr1-40049104;