rs1935885

Variant names:

• chr1-190078695-A-G
• rs1935885

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.6 in 151,566 control chromosomes in the GnomAD database, including 27,997 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 0.60 (27997 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 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: 0.600 AC: 90849 AN: 151446 Hom.: 27932 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.600 AC: 90982 AN: 151566 Hom.: 27997 Cov.: 32 AF XY: 0.602 AC XY: 44595 AN XY: 74078

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.617

Alfa AF: 0.564 Hom.: 4145

Bravo AF: 0.608

Asia WGS AF: 0.616 AC: 2143 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1935885; hg19: chr1-190047825;