rs3954895

Variant names:

• chr8-70547011-C-G
• rs3954895
• ENST00000755107.1:n.593+14611C>G

Variant summary

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

The ENST00000755107.1(ENSG00000298363):​n.593+14611C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,962 control chromosomes in the GnomAD database, including 14,459 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 0.42 (14459 hom., cov: 31)
• Consequence: ENSG00000298363 ENST00000755107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 2 publications found

Genes affected

ENSG00000298363 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 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
ENSG00000298363	ENST00000755107.1	n.593+14611C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63960 AN: 151844 Hom.: 14423 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.422 AC: 64063 AN: 151962 Hom.: 14459 Cov.: 31 AF XY: 0.425 AC XY: 31573 AN XY: 74306

African (AFR) AF: 0.431 AC: 17829 AN: 41408

American (AMR) AF: 0.480 AC: 7333 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3470

East Asian (EAS) AF: 0.899 AC: 4655 AN: 5178

South Asian (SAS) AF: 0.390 AC: 1873 AN: 4808

European-Finnish (FIN) AF: 0.394 AC: 4153 AN: 10548

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26171 AN: 67960

Other (OTH) AF: 0.402 AC: 850 AN: 2114

Alfa AF: 0.398 Hom.: 1494

Bravo AF: 0.434

Asia WGS AF: 0.647 AC: 2248 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	0.52
DANN	Benign	0.34
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs3954895; hg19: chr8-71459246;