rs2227139

Variant names:

• chr6-32445682-G-A
• rs2227139
• ENST00000766007.1:n.163-7422C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-32445682-G-A
• chr6-32445682-G-C
• chr6-32445682-G-T

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.163-7422C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,938 control chromosomes in the GnomAD database, including 29,213 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 0.62 (29213 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.698
• Publications: 63 publications found

Genes affected

ENSG00000299747 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.723 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
ENSG00000299747	ENST00000766007.1	n.163-7422C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93570 AN: 151820 Hom.: 29194 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.616 AC: 93632 AN: 151938 Hom.: 29213 Cov.: 31 AF XY: 0.617 AC XY: 45853 AN XY: 74274

African (AFR) AF: 0.597 AC: 24701 AN: 41380

American (AMR) AF: 0.671 AC: 10260 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2593 AN: 3472

East Asian (EAS) AF: 0.706 AC: 3651 AN: 5170

South Asian (SAS) AF: 0.743 AC: 3581 AN: 4820

European-Finnish (FIN) AF: 0.517 AC: 5443 AN: 10526

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41107 AN: 67978

Other (OTH) AF: 0.651 AC: 1372 AN: 2106

Alfa AF: 0.611 Hom.: 102804

Bravo AF: 0.627

Asia WGS AF: 0.694 AC: 2416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.2
DANN	Benign	0.60
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2227139; hg19: chr6-32413459;