chr6-129575356-G-T

Position:

• chr6-129575356-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665046.1(ENSG00000226149):​n.30+662C>A variant causes a intron, non coding transcript 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: ENST00000665046.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665046.1	n.30+662C>A		intron_variant, non_coding_transcript_variant
	ENST00000657779.1	n.48+20C>A		intron_variant, non_coding_transcript_variant
	ENST00000670413.1	n.48+20C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.203

Alfa AF: 0.209 Hom.: 7314

Bravo AF: 0.226

Asia WGS AF: 0.267 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10457526; hg19: chr6-129896501;