rs6861957

Positions:

• chr5-33936275-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.026 in 155,824 control chromosomes in the GnomAD database, including 78 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 0.026 (72 hom., cov: 33)
  • Exomes 𝑓: 0.035 (6 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0258 (3926/152338) while in subpopulation NFE AF= 0.0367 (2497/68022). AF 95% confidence interval is 0.0355. There are 72 homozygotes in gnomad4. There are 1931 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 72 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0258 AC: 3928 AN: 152220 Hom.: 72 Cov.: 33

Gnomad AFR AF: 0.00617

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0197

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0367

Gnomad OTH AF: 0.0234

GnomAD4 exome AF: 0.0350 AC: 122 AN: 3486 Hom.: 6 AF XY: 0.0365 AC XY: 64 AN XY: 1752

Gnomad4 AFR exome AF: 0.0130

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0543

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0818

Gnomad4 NFE exome AF: 0.0365

Gnomad4 OTH exome AF: 0.0318

GnomAD4 genome AF: 0.0258 AC: 3926 AN: 152338 Hom.: 72 Cov.: 33 AF XY: 0.0259 AC XY: 1931 AN XY: 74504

Gnomad4 AFR AF: 0.00616

Gnomad4 AMR AF: 0.0197

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.0568

Gnomad4 NFE AF: 0.0367

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0327 Hom.: 12

Bravo AF: 0.0232

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6861957; hg19: chr5-33936380;