rs7259376

Variant names:

• chr19-22324903-A-G
• rs7259376

Your query was ambiguous. Multiple possible variants found:

• chr19-22324903-A-G
• chr19-22324903-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 0.556 in 151,970 control chromosomes in the GnomAD database, including 23,773 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 0.56 (23773 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 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: 0.556 AC: 84374 AN: 151852 Hom.: 23739 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.556 AC: 84462 AN: 151970 Hom.: 23773 Cov.: 32 AF XY: 0.563 AC XY: 41810 AN XY: 74294

African (AFR) AF: 0.517 AC: 21427 AN: 41426

American (AMR) AF: 0.574 AC: 8769 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2362 AN: 3472

East Asian (EAS) AF: 0.706 AC: 3644 AN: 5158

South Asian (SAS) AF: 0.760 AC: 3662 AN: 4820

European-Finnish (FIN) AF: 0.553 AC: 5829 AN: 10542

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36953 AN: 67960

Other (OTH) AF: 0.576 AC: 1216 AN: 2112

Alfa AF: 0.542 Hom.: 3806

Bravo AF: 0.548

Asia WGS AF: 0.746 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.81
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7259376; hg19: chr19-22507705;