rs3762867

Variant names:

• chr4-335897-G-A
• rs3762867
• ENST00000653800.3:n.288+1302C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-335897-G-A
• chr4-335897-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653800.3(ENSG00000286705):​n.288+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 ENST00000653800.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• Publications: 5 publications found

Genes affected

ENSG00000286705 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653800.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286705	ENST00000653800.3		n.288+1302C>T		intron	N/A

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

African (AFR) AF: 0.562 AC: 23273 AN: 41444

American (AMR) AF: 0.335 AC: 5117 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1730 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1640 AN: 5174

South Asian (SAS) AF: 0.412 AC: 1982 AN: 4806

European-Finnish (FIN) AF: 0.428 AC: 4520 AN: 10560

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25918 AN: 67960

Other (OTH) AF: 0.423 AC: 889 AN: 2104

Alfa AF: 0.405 Hom.: 2116

Bravo AF: 0.430

Asia WGS AF: 0.387 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.51
PhyloP100		-0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3762867;

hg19: chr4-329686;