rs6676300

Variant names:

• chr1-11865243-A-G
• rs6676300

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 0.417 in 152,088 control chromosomes in the GnomAD database, including 14,574 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 0.42 (14574 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 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: 0.417 AC: 63301 AN: 151970 Hom.: 14536 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.417 AC: 63384 AN: 152088 Hom.: 14574 Cov.: 32 AF XY: 0.410 AC XY: 30494 AN XY: 74376

African (AFR) AF: 0.617 AC: 25588 AN: 41470

American (AMR) AF: 0.275 AC: 4198 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1205 AN: 3466

East Asian (EAS) AF: 0.196 AC: 1010 AN: 5164

South Asian (SAS) AF: 0.446 AC: 2155 AN: 4830

European-Finnish (FIN) AF: 0.301 AC: 3189 AN: 10590

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24717 AN: 67964

Other (OTH) AF: 0.399 AC: 840 AN: 2106

Alfa AF: 0.380 Hom.: 49278

Bravo AF: 0.420

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.29
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs6676300; hg19: chr1-11925300; COSMIC: COSV59923971;