rs1694112

chr6-32681887-T-Achr6-32681887-T-C

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 0.0543 in 152,104 control chromosomes in the GnomAD database, including 313 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 0.054 (313 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0922 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: 0.0542 AC: 8236 AN: 151984 Hom.: 312 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0290

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0543 AC: 8254 AN: 152104 Hom.: 313 Cov.: 32 AF XY: 0.0585 AC XY: 4349 AN XY: 74386

Gnomad4 AFR AF: 0.0696

Gnomad4 AMR AF: 0.0963

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.0135

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0289

Gnomad4 OTH AF: 0.0483

Alfa AF: 0.00915 Hom.: 814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.087
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1694112; hg19: chr6-32649664;