6-129548122-T-G

Position:

• chr6-129548122-T-G

Variant summary

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

The ENST00000665046.1(ENSG00000226149):​n.140-7580A>C 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 0.244 in 151,974 control chromosomes in the GnomAD database, including 4,694 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 0.24 (4694 hom., cov: 32)
• Consequence: ENST00000665046.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723409	XR_001743860.2	n.11510-7580A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665046.1	n.140-7580A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37105 AN: 151854 Hom.: 4695 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.244 AC: 37134 AN: 151974 Hom.: 4694 Cov.: 32 AF XY: 0.244 AC XY: 18134 AN XY: 74274

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.223

Alfa AF: 0.225 Hom.: 8136

Bravo AF: 0.249

Asia WGS AF: 0.366 AC: 1269 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.88
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7760943; hg19: chr6-129869267;