rs3848445

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000230647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000700765.1	n.139+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

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.943

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.970

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.935

Alfa AF: 0.949 Hom.: 149956

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3848445; hg19: chr17-14294021;