rs6677188

Variant names:

• chr1-67274720-T-A
• rs6677188

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 0.277 in 152,062 control chromosomes in the GnomAD database, including 6,162 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 0.28 (6162 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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: 0.277 AC: 42076 AN: 151944 Hom.: 6155 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.277 AC: 42116 AN: 152062 Hom.: 6162 Cov.: 32 AF XY: 0.273 AC XY: 20262 AN XY: 74350

African (AFR) AF: 0.344 AC: 14282 AN: 41458

American (AMR) AF: 0.301 AC: 4605 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 847 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1217 AN: 5172

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4816

European-Finnish (FIN) AF: 0.176 AC: 1864 AN: 10588

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17364 AN: 67970

Other (OTH) AF: 0.269 AC: 566 AN: 2106

Alfa AF: 0.267 Hom.: 728

Bravo AF: 0.291

Asia WGS AF: 0.239 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.91
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs6677188; hg19: chr1-67740403;