chr6-129548363-G-T

Variant names:

• chr6-129548363-G-T
• rs2571588
• ENST00000430296.5:n.47-1871C>A

Variant summary

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

The ENST00000430296.5(ENSG00000226149):​n.47-1871C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,944 control chromosomes in the GnomAD database, including 37,580 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 0.69 (37580 hom., cov: 32)
• Consequence: ENSG00000226149 ENST00000430296.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 4 publications found

Genes affected

ENSG00000226149 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723409	XR_001743859.2	n.11510-7821C>A		intron_variant	Intron 1 of 6
LOC102723409	XR_001743860.2	n.11510-7821C>A		intron_variant	Intron 1 of 7
LOC102723409	XR_007059754.1	n.11510-7821C>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226149	ENST00000430296.5	n.47-1871C>A		intron_variant	Intron 1 of 6	5
ENSG00000226149	ENST00000657779.1	n.158-7821C>A		intron_variant	Intron 2 of 9
ENSG00000226149	ENST00000659721.1	n.47-1735C>A		intron_variant	Intron 1 of 10

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104790 AN: 151826 Hom.: 37527 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.690 AC: 104904 AN: 151944 Hom.: 37580 Cov.: 32 AF XY: 0.697 AC XY: 51768 AN XY: 74254

African (AFR) AF: 0.874 AC: 36252 AN: 41496

American (AMR) AF: 0.707 AC: 10779 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1892 AN: 3462

East Asian (EAS) AF: 0.838 AC: 4328 AN: 5166

South Asian (SAS) AF: 0.793 AC: 3822 AN: 4820

European-Finnish (FIN) AF: 0.604 AC: 6371 AN: 10542

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39213 AN: 67904

Other (OTH) AF: 0.654 AC: 1381 AN: 2112

Alfa AF: 0.622 Hom.: 55152

Bravo AF: 0.703

Asia WGS AF: 0.826 AC: 2872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.81
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2571588; hg19: chr6-129869508; COSMIC: COSV69918039;