rs6683918

Variant names:

• chr1-103904059-G-A
• rs6683918

Your query was ambiguous. Multiple possible variants found:

• chr1-103904059-G-A
• chr1-103904059-G-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 0.143 in 152,132 control chromosomes in the GnomAD database, including 1,848 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 0.14 (1848 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.202 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: 0.144 AC: 21824 AN: 152014 Hom.: 1845 Cov.: 31

Gnomad AFR AF: 0.0482

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.143 AC: 21828 AN: 152132 Hom.: 1848 Cov.: 31 AF XY: 0.143 AC XY: 10633 AN XY: 74376

African (AFR) AF: 0.0482 AC: 2001 AN: 41530

American (AMR) AF: 0.208 AC: 3178 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0836 AC: 290 AN: 3468

East Asian (EAS) AF: 0.125 AC: 647 AN: 5162

South Asian (SAS) AF: 0.148 AC: 714 AN: 4822

European-Finnish (FIN) AF: 0.172 AC: 1818 AN: 10566

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.186 AC: 12671 AN: 67984

Other (OTH) AF: 0.145 AC: 307 AN: 2112

Alfa AF: 0.160 Hom.: 2169

Bravo AF: 0.141

Asia WGS AF: 0.153 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.74
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs6683918; hg19: chr1-104446681;