chr6-129540247-T-C

Position:

• chr6-129540247-T-C

Variant summary

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

The ENST00000665046.1(ENSG00000226149):​n.235+200A>G 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 0.351 in 152,016 control chromosomes in the GnomAD database, including 10,147 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 0.35 (10147 hom., cov: 32)
• Consequence: ENST00000665046.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723409	XR_001743860.2	n.11605+200A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665046.1	n.235+200A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53274 AN: 151896 Hom.: 10144 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.351 AC: 53306 AN: 152016 Hom.: 10147 Cov.: 32 AF XY: 0.353 AC XY: 26231 AN XY: 74306

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.326

Alfa AF: 0.275 Hom.: 13043

Bravo AF: 0.349

Asia WGS AF: 0.458 AC: 1591 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0010
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2275215; hg19: chr6-129861392;