rs10045431

Positions:

• chr5-159387525-A-C
• chr5-159387525-A-T

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.283-5008A>C 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 0.782 in 152,060 control chromosomes in the GnomAD database, including 46,796 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 0.78 (46796 hom., cov: 32)
• Consequence: ENST00000635333.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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
	ENST00000635333.1	n.283-5008A>C		intron_variant, non_coding_transcript_variant		5
	ENST00000641150.1	n.533-28999A>C		intron_variant, non_coding_transcript_variant
	ENST00000648969.1	n.54-28999A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118711 AN: 151942 Hom.: 46727 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.782 AC: 118844 AN: 152060 Hom.: 46796 Cov.: 32 AF XY: 0.788 AC XY: 58590 AN XY: 74320

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.770

Alfa AF: 0.721 Hom.: 89943

Bravo AF: 0.787

Asia WGS AF: 0.884 AC: 3076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10045431; hg19: chr5-158814533;