rs1571631

Variant names:

• chr6-108528898-C-T
• rs1571631
• ENST00000659932.2:n.136+29266G>A

Variant summary

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

The ENST00000659932.2(ENSG00000287044):​n.136+29266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,064 control chromosomes in the GnomAD database, including 23,834 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 0.56 (23834 hom., cov: 33)
• Consequence: ENSG00000287044 ENST00000659932.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 3 publications found

Genes affected

ENSG00000287044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659932.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287044	ENST00000659932.2		n.136+29266G>A		intron	N/A
	ENSG00000287044	ENST00000784390.1		n.119+29266G>A		intron	N/A
	ENSG00000287044	ENST00000784391.1		n.127-27270G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84535 AN: 151946 Hom.: 23804 Cov.: 33

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.556 AC: 84617 AN: 152064 Hom.: 23834 Cov.: 33 AF XY: 0.557 AC XY: 41427 AN XY: 74324

African (AFR) AF: 0.643 AC: 26642 AN: 41454

American (AMR) AF: 0.534 AC: 8162 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1981 AN: 3470

East Asian (EAS) AF: 0.394 AC: 2033 AN: 5162

South Asian (SAS) AF: 0.646 AC: 3118 AN: 4830

European-Finnish (FIN) AF: 0.525 AC: 5535 AN: 10552

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35267 AN: 67994

Other (OTH) AF: 0.565 AC: 1194 AN: 2112

Alfa AF: 0.530 Hom.: 14782

Bravo AF: 0.556

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.59
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1571631; hg19: chr6-108850101;