chr6-29703963-G-A

Variant names:

• chr6-29703963-G-A
• rs3131866
• ENST00000850325.1:n.220-4477G>A

Variant summary

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

The ENST00000850325.1(ENSG00000310484):​n.220-4477G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,842 control chromosomes in the GnomAD database, including 4,826 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 0.25 (4826 hom., cov: 31)
• Consequence: ENSG00000310484 ENST00000850325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 11 publications found

Genes affected

ENSG00000310484 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 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
ENSG00000310484	ENST00000850325.1	n.220-4477G>A		intron_variant	Intron 1 of 2
ENSG00000310484	ENST00000850326.1	n.202-4477G>A		intron_variant	Intron 1 of 1
ENSG00000310484	ENST00000850327.1	n.122+1126G>A		intron_variant	Intron 1 of 2
ENSG00000310484	ENST00000850328.1	n.122+1126G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37601 AN: 151724 Hom.: 4808 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.248 AC: 37642 AN: 151842 Hom.: 4826 Cov.: 31 AF XY: 0.244 AC XY: 18117 AN XY: 74220

African (AFR) AF: 0.230 AC: 9509 AN: 41378

American (AMR) AF: 0.279 AC: 4257 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 632 AN: 3462

East Asian (EAS) AF: 0.348 AC: 1793 AN: 5154

South Asian (SAS) AF: 0.335 AC: 1611 AN: 4810

European-Finnish (FIN) AF: 0.148 AC: 1562 AN: 10528

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17435 AN: 67942

Other (OTH) AF: 0.253 AC: 532 AN: 2102

Alfa AF: 0.254 Hom.: 8389

Bravo AF: 0.254

Asia WGS AF: 0.414 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.48
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs3131866; hg19: chr6-29671740;