rs3762867

chr4-335897-G-Achr4-335897-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, non coding transcript 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: ENST00000653800.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000653800.2	n.241+1302C>T		intron_variant, non_coding_transcript_variant

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;