rs4495224

Positions:

• chr5-40477413-C-A
• chr5-40477413-C-G

Variant summary

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

The ENST00000648975.1(ENSG00000285616):​n.2650+450G>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 0.606 in 151,828 control chromosomes in the GnomAD database, including 28,502 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 0.61 (28502 hom., cov: 31)
• Consequence: ENST00000648975.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 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
	ENST00000648975.1	n.2650+450G>T		intron_variant, non_coding_transcript_variant
	ENST00000649444.1	n.120-8963C>A		intron_variant, non_coding_transcript_variant
	ENST00000649894.1	n.119+13733C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91977 AN: 151710 Hom.: 28474 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.606 AC: 92056 AN: 151828 Hom.: 28502 Cov.: 31 AF XY: 0.599 AC XY: 44406 AN XY: 74162

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.622

Alfa AF: 0.646 Hom.: 4982

Bravo AF: 0.607

Asia WGS AF: 0.400 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	4.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4495224; hg19: chr5-40477515;