rs3923114

Positions:

• chr5-69030471-T-C

Variant summary

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

The ENST00000696797.1(ENSG00000249335):​n.466+8048A>G 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 0.298 in 152,110 control chromosomes in the GnomAD database, including 8,645 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 0.30 (8645 hom., cov: 32)
• Consequence: ENST00000696797.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.425 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
	ENST00000696797.1	n.466+8048A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45378 AN: 151992 Hom.: 8647 Cov.: 32

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.298 AC: 45374 AN: 152110 Hom.: 8645 Cov.: 32 AF XY: 0.294 AC XY: 21844 AN XY: 74362

Gnomad4 AFR AF: 0.0792

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.327

Alfa AF: 0.338 Hom.: 1231

Bravo AF: 0.301

Asia WGS AF: 0.182 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3923114; hg19: chr5-68326298;