rs4865673

Positions:

• chr5-51632976-G-A

Variant summary

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

The ENST00000666280.1(ENSG00000288035):​n.435+31638C>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 0.289 in 151,978 control chromosomes in the GnomAD database, including 6,636 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 0.29 (6636 hom., cov: 32)
• Consequence: ENST00000666280.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 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
	ENST00000666280.1	n.435+31638C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43976 AN: 151858 Hom.: 6631 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.0703

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.289 AC: 43997 AN: 151978 Hom.: 6636 Cov.: 32 AF XY: 0.285 AC XY: 21192 AN XY: 74270

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.0707

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.286

Alfa AF: 0.314 Hom.: 15638

Bravo AF: 0.289

Asia WGS AF: 0.173 AC: 602 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.6
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4865673; hg19: chr5-50928810;