6-29644108-T-C

Variant names:

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

Variant summary

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

The ENST00000782059.1(ENSG00000301820):​n.436-7918A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,156 control chromosomes in the GnomAD database, including 46,850 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 0.78 (46850 hom., cov: 33)
• Consequence: ENSG00000301820 ENST00000782059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 24 publications found

Genes affected

ENSG00000301820 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 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
ENSG00000301820	ENST00000782059.1	n.436-7918A>G		intron_variant	Intron 2 of 2
ENSG00000301820	ENST00000782060.1	n.432-7918A>G		intron_variant	Intron 2 of 2
ENSG00000301820	ENST00000782061.1	n.312-7918A>G		intron_variant	Intron 1 of 1
ENSG00000301820	ENST00000782062.1	n.354-7918A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119071 AN: 152038 Hom.: 46808 Cov.: 33

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.783 AC: 119170 AN: 152156 Hom.: 46850 Cov.: 33 AF XY: 0.780 AC XY: 58036 AN XY: 74390

African (AFR) AF: 0.781 AC: 32430 AN: 41520

American (AMR) AF: 0.830 AC: 12685 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2734 AN: 3472

East Asian (EAS) AF: 0.850 AC: 4399 AN: 5178

South Asian (SAS) AF: 0.763 AC: 3683 AN: 4828

European-Finnish (FIN) AF: 0.671 AC: 7092 AN: 10576

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53559 AN: 67984

Other (OTH) AF: 0.782 AC: 1654 AN: 2114

Alfa AF: 0.792 Hom.: 175555

Bravo AF: 0.796

Asia WGS AF: 0.827 AC: 2879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.19
DANN	Benign	0.31
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;