rs3848445

Variant names:

• chr17-14390704-C-T
• rs3848445
• ENST00000436469.1:n.324-6358C>T

Variant summary

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

The ENST00000436469.1(ENSG00000230647):​n.324-6358C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 152,112 control chromosomes in the GnomAD database, including 64,713 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 0.92 (64713 hom., cov: 30)
• Consequence: ENSG00000230647 ENST00000436469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 13 publications found

Genes affected

ENSG00000230647 (HGNC:58488):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.957 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
ENSG00000230647	ENST00000436469.1	n.324-6358C>T		intron_variant	Intron 3 of 4	5
ENSG00000230647	ENST00000655690.1	n.183-6358C>T		intron_variant	Intron 2 of 3
ENSG00000230647	ENST00000700765.2	n.157+8603C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.920 AC: 139896 AN: 151994 Hom.: 64658 Cov.: 30

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.920 AC: 140009 AN: 152112 Hom.: 64713 Cov.: 30 AF XY: 0.919 AC XY: 68327 AN XY: 74358

African (AFR) AF: 0.864 AC: 35826 AN: 41474

American (AMR) AF: 0.932 AC: 14241 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.943 AC: 3272 AN: 3470

East Asian (EAS) AF: 0.679 AC: 3484 AN: 5128

South Asian (SAS) AF: 0.880 AC: 4244 AN: 4820

European-Finnish (FIN) AF: 0.970 AC: 10289 AN: 10604

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65526 AN: 68020

Other (OTH) AF: 0.935 AC: 1970 AN: 2108

Alfa AF: 0.944 Hom.: 294048

Bravo AF: 0.914

Asia WGS AF: 0.801 AC: 2782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.70
DANN	Benign	0.65
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs3848445; hg19: chr17-14294021;