chr6-32898134-G-A

Position:

• chr6-32898134-G-A

Variant summary

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

The NR_037177.1(LOC100294145):​n.852-2786G>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 0.232 in 152,110 control chromosomes in the GnomAD database, including 4,221 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 0.23 (4221 hom., cov: 31)
• Consequence: LOC100294145 NR_037177.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

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 (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100294145	NR_037177.1	n.852-2786G>A		intron_variant, non_coding_transcript_variant
LOC100294145	NR_037178.1	n.753-2786G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701517.1	n.630-2786G>A		intron_variant, non_coding_transcript_variant
	ENST00000685247.2	n.714-2786G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35274 AN: 151992 Hom.: 4225 Cov.: 31

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.232 AC: 35271 AN: 152110 Hom.: 4221 Cov.: 31 AF XY: 0.226 AC XY: 16835 AN XY: 74370

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.250

Alfa AF: 0.263 Hom.: 7388

Bravo AF: 0.227

Asia WGS AF: 0.201 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
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: rs9276915; hg19: chr6-32865911;