chr6-31705659-G-A

Variant names:

• chr6-31705659-G-A
• rs9267546
• ENST00000461287.1:n.538-3529C>T

Variant summary

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

The ENST00000461287.1(ENSG00000204422):​n.538-3529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,202 control chromosomes in the GnomAD database, including 1,942 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 0.14 (1942 hom., cov: 32)
• Consequence: ENSG00000204422 ENST00000461287.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 29 publications found

Genes affected

ENSG00000204422 (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 = 0.244 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
ENSG00000204422	ENST00000461287.1	n.538-3529C>T		intron_variant	Intron 3 of 21	2

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21665 AN: 152084 Hom.: 1941 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0934

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.142 AC: 21676 AN: 152202 Hom.: 1942 Cov.: 32 AF XY: 0.140 AC XY: 10437 AN XY: 74426

African (AFR) AF: 0.248 AC: 10313 AN: 41504

American (AMR) AF: 0.117 AC: 1791 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 623 AN: 3470

East Asian (EAS) AF: 0.0940 AC: 487 AN: 5180

South Asian (SAS) AF: 0.129 AC: 623 AN: 4832

European-Finnish (FIN) AF: 0.0837 AC: 888 AN: 10606

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.0948 AC: 6449 AN: 68008

Other (OTH) AF: 0.162 AC: 342 AN: 2116

Alfa AF: 0.112 Hom.: 2504

Bravo AF: 0.151

Asia WGS AF: 0.107 AC: 371 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	1.4
DANN	Benign	0.47
PhyloP100		-0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9267546; hg19: chr6-31673436;