rs1885628

Variant names:

• chr6-153941803-G-A
• rs1885628

Your query was ambiguous. Multiple possible variants found:

• chr6-153941803-G-A
• chr6-153941803-G-C
• chr6-153941803-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 0.237 in 152,116 control chromosomes in the GnomAD database, including 4,550 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 0.24 (4550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 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: 0.237 AC: 35957 AN: 151998 Hom.: 4541 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.237 AC: 35979 AN: 152116 Hom.: 4550 Cov.: 32 AF XY: 0.245 AC XY: 18224 AN XY: 74370

African (AFR) AF: 0.184 AC: 7622 AN: 41500

American (AMR) AF: 0.396 AC: 6053 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1696 AN: 5170

South Asian (SAS) AF: 0.387 AC: 1865 AN: 4822

European-Finnish (FIN) AF: 0.237 AC: 2505 AN: 10564

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14436 AN: 67980

Other (OTH) AF: 0.269 AC: 569 AN: 2114

Alfa AF: 0.161 Hom.: 482

Bravo AF: 0.241

Asia WGS AF: 0.380 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.66
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1885628; hg19: chr6-154262938;