rs1891320

Variant names:

• chr1-19970618-C-T
• rs1891320

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 0.198 in 152,086 control chromosomes in the GnomAD database, including 3,619 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 0.20 (3619 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 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: 0.198 AC: 30056 AN: 151968 Hom.: 3617 Cov.: 32

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.198 AC: 30067 AN: 152086 Hom.: 3619 Cov.: 32 AF XY: 0.194 AC XY: 14443 AN XY: 74342

Gnomad4 AFR AF: 0.0753

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.208

Alfa AF: 0.243 Hom.: 2461

Bravo AF: 0.183

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.48
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891320; hg19: chr1-20297111;