rs3131854

Variant names:

• chr6-29644108-T-A
• rs3131854
• ENST00000782059.1:n.436-7918A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-29644108-T-A
• chr6-29644108-T-C
• chr6-29644108-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000782059.1(ENSG00000301820):​n.436-7918A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: ENSG00000301820 ENST00000782059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 0 publications found

Genes affected

ENSG00000301820 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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
ENSG00000301820	ENST00000782059.1	n.436-7918A>T		intron_variant	Intron 2 of 2
ENSG00000301820	ENST00000782060.1	n.432-7918A>T		intron_variant	Intron 2 of 2
ENSG00000301820	ENST00000782061.1	n.312-7918A>T		intron_variant	Intron 1 of 1
ENSG00000301820	ENST00000782062.1	n.354-7918A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.50
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs3131854; hg19: chr6-29611885;