rs1935885

Variant names:

• chr1-190078695-A-G
• rs1935885

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 0.6 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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

African (AFR) AF: 0.741 AC: 30719 AN: 41464

American (AMR) AF: 0.602 AC: 9141 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2027 AN: 3462

East Asian (EAS) AF: 0.494 AC: 2550 AN: 5162

South Asian (SAS) AF: 0.651 AC: 3134 AN: 4814

European-Finnish (FIN) AF: 0.556 AC: 5863 AN: 10552

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35503 AN: 67624

Other (OTH) AF: 0.617 AC: 1296 AN: 2100

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
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs1935885; hg19: chr1-190047825;