rs3848445

Positions:

• chr17-14390704-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000700765.1(ENSG00000230647):​n.139+8603C>T variant causes a intron, non coding transcript 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: ENST00000700765.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000700765.1	n.139+8603C>T		intron_variant, non_coding_transcript_variant
	ENST00000436469.1	n.324-6358C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000655690.1	n.183-6358C>T		intron_variant, non_coding_transcript_variant

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;