rs1609717

Variant names:

• chr19-4519438-G-A
• rs1609717

Your query was ambiguous. Multiple possible variants found:

• chr19-4519438-G-A
• chr19-4519438-G-C

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 0.951 in 152,208 control chromosomes in the GnomAD database, including 68,927 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 0.95 (68927 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.953 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: 0.951 AC: 144713 AN: 152090 Hom.: 68878 Cov.: 33

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.951 AC: 144820 AN: 152208 Hom.: 68927 Cov.: 33 AF XY: 0.950 AC XY: 70738 AN XY: 74426

African (AFR) AF: 0.958 AC: 39804 AN: 41560

American (AMR) AF: 0.962 AC: 14716 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3307 AN: 3472

East Asian (EAS) AF: 0.976 AC: 5016 AN: 5140

South Asian (SAS) AF: 0.900 AC: 4344 AN: 4824

European-Finnish (FIN) AF: 0.945 AC: 10029 AN: 10618

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64412 AN: 67982

Other (OTH) AF: 0.954 AC: 2016 AN: 2114

Alfa AF: 0.951 Hom.: 93816

Bravo AF: 0.956

Asia WGS AF: 0.943 AC: 3280 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	0.039
DANN	Benign	0.53
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1609717; hg19: chr19-4519450;