rs1986655

Variant names:

• chr4-125072347-A-G
• rs1986655

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 0.131 in 152,130 control chromosomes in the GnomAD database, including 1,664 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 0.13 (1664 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 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: 0.131 AC: 19948 AN: 152010 Hom.: 1663 Cov.: 32

Gnomad AFR AF: 0.0415

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.131 AC: 19957 AN: 152130 Hom.: 1664 Cov.: 32 AF XY: 0.139 AC XY: 10336 AN XY: 74370

African (AFR) AF: 0.0415 AC: 1722 AN: 41540

American (AMR) AF: 0.147 AC: 2247 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3470

East Asian (EAS) AF: 0.193 AC: 1001 AN: 5174

South Asian (SAS) AF: 0.255 AC: 1230 AN: 4826

European-Finnish (FIN) AF: 0.204 AC: 2155 AN: 10564

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10425 AN: 67972

Other (OTH) AF: 0.136 AC: 286 AN: 2110

Alfa AF: 0.143 Hom.: 3511

Bravo AF: 0.119

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.79
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs1986655; hg19: chr4-125993502;