rs210937

Positions:

• chr6-135219242-G-A

Variant summary

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

The variant allele was found at a frequency of 0.581 in 186,856 control chromosomes in the GnomAD database, including 34,391 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 0.60 (30120 hom., cov: 33)
  • Exomes 𝑓: 0.49 (4271 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.135219242G>A		intergenic_region
LOC105378011	XR_001744368.2	n.177-3742C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91357 AN: 152016 Hom.: 30061 Cov.: 33

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.520

GnomAD4 exome AF: 0.490 AC: 17011 AN: 34722 Hom.: 4271 AF XY: 0.491 AC XY: 7889 AN XY: 16054

Gnomad4 AFR exome AF: 0.871

Gnomad4 AMR exome AF: 0.425

Gnomad4 ASJ exome AF: 0.373

Gnomad4 EAS exome AF: 0.451

Gnomad4 SAS exome AF: 0.546

Gnomad4 FIN exome AF: 0.593

Gnomad4 NFE exome AF: 0.492

Gnomad4 OTH exome AF: 0.488

GnomAD4 genome AF: 0.601 AC: 91481 AN: 152134 Hom.: 30120 Cov.: 33 AF XY: 0.600 AC XY: 44622 AN XY: 74352

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.526

Alfa AF: 0.503 Hom.: 33181

Bravo AF: 0.597

Asia WGS AF: 0.549 AC: 1908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs210937; hg19: chr6-135540380; COSMIC: COSV57197014;