ENST00000849353.1:n.102+3865G>C

Variant names:

• chr13-26727717-G-C
• rs2441075
• ENST00000849353.1:n.102+3865G>C

Variant summary

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

The ENST00000849353.1(ENSG00000310371):​n.102+3865G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 150,996 control chromosomes in the GnomAD database, including 17,082 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 0.47 (17082 hom., cov: 32)
• Consequence: ENSG00000310371 ENST00000849353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 1 publications found

Genes affected

ENSG00000310371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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
ENSG00000310371	ENST00000849353.1	n.102+3865G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71143 AN: 150880 Hom.: 17065 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.471 AC: 71194 AN: 150996 Hom.: 17082 Cov.: 32 AF XY: 0.469 AC XY: 34597 AN XY: 73696

African (AFR) AF: 0.360 AC: 14797 AN: 41090

American (AMR) AF: 0.494 AC: 7519 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2126 AN: 3462

East Asian (EAS) AF: 0.614 AC: 3167 AN: 5156

South Asian (SAS) AF: 0.530 AC: 2542 AN: 4796

European-Finnish (FIN) AF: 0.411 AC: 4217 AN: 10252

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35131 AN: 67722

Other (OTH) AF: 0.512 AC: 1077 AN: 2104

Alfa AF: 0.318 Hom.: 762

Bravo AF: 0.469

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.68
DANN	Benign	0.60
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2441075; hg19: chr13-27301854;