rs6695104

Variant names:

• chr1-247897592-C-A
• rs6695104

Your query was ambiguous. Multiple possible variants found:

• chr1-247897592-C-A
• chr1-247897592-C-G
• chr1-247897592-C-T

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 0.251 in 152,028 control chromosomes in the GnomAD database, including 5,373 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 0.25 (5373 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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: 0.251 AC: 38177 AN: 151910 Hom.: 5364 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.251 AC: 38230 AN: 152028 Hom.: 5373 Cov.: 32 AF XY: 0.253 AC XY: 18788 AN XY: 74314

African (AFR) AF: 0.355 AC: 14687 AN: 41420

American (AMR) AF: 0.294 AC: 4492 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2119 AN: 5162

South Asian (SAS) AF: 0.265 AC: 1272 AN: 4806

European-Finnish (FIN) AF: 0.174 AC: 1837 AN: 10582

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12463 AN: 68006

Other (OTH) AF: 0.254 AC: 536 AN: 2112

Alfa AF: 0.194 Hom.: 2198

Bravo AF: 0.269

Asia WGS AF: 0.352 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.88
DANN	Benign	0.47
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6695104; hg19: chr1-248060894;