chr6-87933354-A-G

Position:

• chr6-87933354-A-G

Variant summary

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

The XR_001744246.1(LOC105377882):​n.203+1711A>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 0.506 in 152,074 control chromosomes in the GnomAD database, including 21,009 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 0.51 (21009 hom., cov: 32)
• Consequence: LOC105377882 XR_001744246.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

Genes affected

LOC105377882 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377882	XR_001744246.1	n.203+1711A>G		intron_variant, non_coding_transcript_variant
LOC105377882	XR_002956400.1	n.203+1711A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76974 AN: 151956 Hom.: 21024 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.506 AC: 76981 AN: 152074 Hom.: 21009 Cov.: 32 AF XY: 0.505 AC XY: 37537 AN XY: 74328

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.539

Alfa AF: 0.591 Hom.: 55947

Bravo AF: 0.491

Asia WGS AF: 0.405 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4235835; hg19: chr6-88643072;