rs3762867

Variant names:

• chr4-335897-G-A
• rs3762867
• ENST00000653800.2:n.241+1302C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-335897-G-A
• chr4-335897-G-T

Variant summary

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

The ENST00000653800.2(ENSG00000286705):​n.241+1302C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,002 control chromosomes in the GnomAD database, including 14,731 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 0.43 (14731 hom., cov: 32)
• Consequence: ENSG00000286705 ENST00000653800.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

Genes affected

ENSG00000286705 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 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
ENSG00000286705	ENST00000653800.2	n.241+1302C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65477 AN: 151884 Hom.: 14715 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.431 AC: 65522 AN: 152002 Hom.: 14731 Cov.: 32 AF XY: 0.430 AC XY: 31979 AN XY: 74284

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.423

Alfa AF: 0.400 Hom.: 1987

Bravo AF: 0.430

Asia WGS AF: 0.387 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3762867; hg19: chr4-329686;