6-129575356-G-T

Variant names:

• chr6-129575356-G-T
• rs10457526
• ENST00000657779.1:n.48+20C>A

Variant summary

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

The ENST00000657779.1(ENSG00000226149):​n.48+20C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,992 control chromosomes in the GnomAD database, including 3,960 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 0.22 (3960 hom., cov: 31)
• Consequence: ENSG00000226149 ENST00000657779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 9 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657779.1. 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
	ENSG00000226149	ENST00000657779.1		n.48+20C>A		intron	N/A
	ENSG00000226149	ENST00000665046.1		n.30+662C>A		intron	N/A
	ENSG00000226149	ENST00000670413.1		n.48+20C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33551 AN: 151874 Hom.: 3954 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.221 AC: 33568 AN: 151992 Hom.: 3960 Cov.: 31 AF XY: 0.226 AC XY: 16788 AN XY: 74292

African (AFR) AF: 0.200 AC: 8282 AN: 41470

American (AMR) AF: 0.334 AC: 5102 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3466

East Asian (EAS) AF: 0.262 AC: 1353 AN: 5162

South Asian (SAS) AF: 0.305 AC: 1473 AN: 4824

European-Finnish (FIN) AF: 0.215 AC: 2269 AN: 10538

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.204 AC: 13851 AN: 67954

Other (OTH) AF: 0.203 AC: 429 AN: 2112

Alfa AF: 0.211 Hom.: 15628

Bravo AF: 0.226

Asia WGS AF: 0.267 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.59
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10457526; hg19: chr6-129896501;