rs1694112

Variant names:

• chr6-32681887-T-A
• rs1694112

Your query was ambiguous. Multiple possible variants found:

• chr6-32681887-T-A
• chr6-32681887-T-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0696 AC: 2889 AN: 41480

American (AMR) AF: 0.0963 AC: 1472 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3472

East Asian (EAS) AF: 0.0881 AC: 456 AN: 5178

South Asian (SAS) AF: 0.0135 AC: 65 AN: 4812

European-Finnish (FIN) AF: 0.113 AC: 1192 AN: 10570

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0289 AC: 1968 AN: 67996

Other (OTH) AF: 0.0483 AC: 102 AN: 2112

Alfa AF: 0.00415 Hom.: 2358

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1694112; hg19: chr6-32649664;