10-4768369-A-G

Variant names:

• chr10-4768369-A-G
• rs1901633
• ENST00000670284.1:n.320-3855T>C

Variant summary

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

The ENST00000670284.1(ENSG00000287023):​n.320-3855T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,994 control chromosomes in the GnomAD database, including 6,825 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 0.28 (6825 hom., cov: 32)
• Consequence: ENSG00000287023 ENST00000670284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

ENSG00000287023 (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 = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287023	ENST00000670284.1	n.320-3855T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42696 AN: 151876 Hom.: 6810 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.281 AC: 42737 AN: 151994 Hom.: 6825 Cov.: 32 AF XY: 0.290 AC XY: 21543 AN XY: 74282

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.282

Alfa AF: 0.287 Hom.: 3827

Bravo AF: 0.272

Asia WGS AF: 0.305 AC: 1060 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	1.0
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1901633; hg19: chr10-4810561;