rs884164

Variant names:

• chr19-4521613-A-G
• rs884164

Your query was ambiguous. Multiple possible variants found:

• chr19-4521613-A-G
• chr19-4521613-A-T

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 0.199 in 151,912 control chromosomes in the GnomAD database, including 6,248 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 (6248 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 15 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 = 0.523 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: 30104 AN: 151792 Hom.: 6225 Cov.: 31

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.199 AC: 30182 AN: 151912 Hom.: 6248 Cov.: 31 AF XY: 0.191 AC XY: 14205 AN XY: 74254

African (AFR) AF: 0.528 AC: 21871 AN: 41384

American (AMR) AF: 0.112 AC: 1706 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3466

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5160

South Asian (SAS) AF: 0.0435 AC: 209 AN: 4806

European-Finnish (FIN) AF: 0.0478 AC: 505 AN: 10572

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0734 AC: 4984 AN: 67940

Other (OTH) AF: 0.163 AC: 343 AN: 2108

Alfa AF: 0.128 Hom.: 5923

Bravo AF: 0.219

Asia WGS AF: 0.0620 AC: 217 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	0.29
DANN	Benign	0.61
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs884164; hg19: chr19-4521625;