rs6675798

Variant names:

• chr1-1241217-T-C
• rs6675798

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 0.158 in 152,118 control chromosomes in the GnomAD database, including 2,564 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 0.16 (2564 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 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: 0.157 AC: 23933 AN: 152000 Hom.: 2539 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0879

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0976

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.158 AC: 24007 AN: 152118 Hom.: 2564 Cov.: 33 AF XY: 0.159 AC XY: 11825 AN XY: 74354

African (AFR) AF: 0.304 AC: 12598 AN: 41496

American (AMR) AF: 0.0877 AC: 1341 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3468

East Asian (EAS) AF: 0.182 AC: 935 AN: 5144

South Asian (SAS) AF: 0.129 AC: 623 AN: 4830

European-Finnish (FIN) AF: 0.111 AC: 1174 AN: 10606

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0976 AC: 6630 AN: 67960

Other (OTH) AF: 0.132 AC: 279 AN: 2112

Alfa AF: 0.110 Hom.: 1753

Bravo AF: 0.164

Asia WGS AF: 0.168 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6675798; hg19: chr1-1176597; COSMIC: COSV57803500;