rs10440635

chr5-40490688-G-A

Variant summary

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

The ENST00000649444.1(ENSG00000285552):n.242+4190G>A 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 0.548 in 151,928 control chromosomes in the GnomAD database, including 23,473 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 0.55 (23473 hom., cov: 32)
• Consequence: ENST00000649444.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.775

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649444.1	n.242+4190G>A		intron_variant, non_coding_transcript_variant
	ENST00000649894.1	n.120-13183G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83160 AN: 151810 Hom.: 23445 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.548 AC: 83231 AN: 151928 Hom.: 23473 Cov.: 32 AF XY: 0.537 AC XY: 39856 AN XY: 74240

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.528

Alfa AF: 0.564 Hom.: 44206

Bravo AF: 0.554

Asia WGS AF: 0.265 AC: 924 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.5
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10440635; hg19: chr5-40490790;