rs996005

chr6-96727225-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The variant allele was found at a frequency of 0.0113 in 152,326 control chromosomes in the GnomAD database, including 23 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 0.011 (23 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0113 (1717/152326) while in subpopulation NFE AF= 0.0198 (1344/68014). AF 95% confidence interval is 0.0189. There are 23 homozygotes in gnomad4. There are 794 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 23 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: 0.0113 AC: 1717 AN: 152208 Hom.: 23 Cov.: 33

Gnomad AFR AF: 0.00292

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.00622

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00866

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0115

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

GnomAD4 genome AF: 0.0113 AC: 1717 AN: 152326 Hom.: 23 Cov.: 33 AF XY: 0.0107 AC XY: 794 AN XY: 74484

Gnomad4 AFR AF: 0.00291

Gnomad4 AMR AF: 0.00621

Gnomad4 ASJ AF: 0.00750

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.00866

Gnomad4 NFE AF: 0.0198

Gnomad4 OTH AF: 0.0113

Alfa AF: 0.0151 Hom.: 1

Bravo AF: 0.0110

Asia WGS AF: 0.000289 AC: 1 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
Cadd	Benign	13
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs996005; hg19: chr6-97175101;