rs10027488

Variant names:

• chr4-186186695-A-G
• rs10027488

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 0.505 in 152,038 control chromosomes in the GnomAD database, including 19,903 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 0.50 (19903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.577 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: 0.505 AC: 76719 AN: 151920 Hom.: 19888 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.505 AC: 76764 AN: 152038 Hom.: 19903 Cov.: 32 AF XY: 0.495 AC XY: 36756 AN XY: 74320

African (AFR) AF: 0.440 AC: 18256 AN: 41446

American (AMR) AF: 0.461 AC: 7034 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1725 AN: 3466

East Asian (EAS) AF: 0.303 AC: 1566 AN: 5172

South Asian (SAS) AF: 0.412 AC: 1988 AN: 4822

European-Finnish (FIN) AF: 0.472 AC: 4988 AN: 10568

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39565 AN: 67986

Other (OTH) AF: 0.520 AC: 1096 AN: 2108

Alfa AF: 0.547 Hom.: 49120

Bravo AF: 0.500

Asia WGS AF: 0.376 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.41
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs10027488; hg19: chr4-187107849;