6-43420316-G-A

Position:

• chr6-43420316-G-A

Variant summary

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

The ENST00000657856.1(ENSG00000287055):​n.1037+2875G>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 0.292 in 152,112 control chromosomes in the GnomAD database, including 6,556 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 0.29 (6556 hom., cov: 32)
• Consequence: ENST00000657856.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375065	XR_007059585.1	n.1106+2875G>A		intron_variant, non_coding_transcript_variant
LOC105375065	XR_001744123.2	n.4198+2875G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657856.1	n.1037+2875G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44370 AN: 151994 Hom.: 6546 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.292 AC: 44405 AN: 152112 Hom.: 6556 Cov.: 32 AF XY: 0.291 AC XY: 21602 AN XY: 74354

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.303

Alfa AF: 0.287 Hom.: 10973

Bravo AF: 0.296

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6907066; hg19: chr6-43388054;