rs41297589

Positions:

• chr6-31575485-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.00765 in 538,866 control chromosomes in the GnomAD database, including 232 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 0.0032 (17 hom., cov: 31)
  • Exomes 𝑓: 0.0094 (215 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.42

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.059 is higher than 0.05.

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: 0.00316 AC: 481 AN: 152046 Hom.: 18 Cov.: 31

Gnomad AFR AF: 0.000314

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00131

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.00483

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00141

Gnomad OTH AF: 0.00383

GnomAD4 exome AF: 0.00942 AC: 3642 AN: 386702 Hom.: 215 AF XY: 0.0141 AC XY: 2856 AN XY: 203072

Gnomad4 AFR exome AF: 0.000282

Gnomad4 AMR exome AF: 0.000748

Gnomad4 ASJ exome AF: 0.000809

Gnomad4 EAS exome AF: 0.00133

Gnomad4 SAS exome AF: 0.0873

Gnomad4 FIN exome AF: 0.000147

Gnomad4 NFE exome AF: 0.00159

Gnomad4 OTH exome AF: 0.00385

GnomAD4 genome AF: 0.00315 AC: 480 AN: 152164 Hom.: 17 Cov.: 31 AF XY: 0.00425 AC XY: 316 AN XY: 74384

Gnomad4 AFR AF: 0.000313

Gnomad4 AMR AF: 0.00131

Gnomad4 ASJ AF: 0.000577

Gnomad4 EAS AF: 0.00465

Gnomad4 SAS AF: 0.0649

Gnomad4 FIN AF: 0.000189

Gnomad4 NFE AF: 0.00141

Gnomad4 OTH AF: 0.00379

Alfa AF: 0.00164 Hom.: 1

Bravo AF: 0.00142

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	20
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41297589; hg19: chr6-31543262;