rs6509942

Variant names:

• chr19-30064044-A-T
• rs6509942

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 0.884 in 152,278 control chromosomes in the GnomAD database, including 60,456 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 0.88 (60456 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• 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 = 0.97 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: 0.884 AC: 134559 AN: 152160 Hom.: 60425 Cov.: 34

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.884 AC: 134642 AN: 152278 Hom.: 60456 Cov.: 34 AF XY: 0.889 AC XY: 66218 AN XY: 74464

African (AFR) AF: 0.711 AC: 29541 AN: 41542

American (AMR) AF: 0.925 AC: 14149 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3335 AN: 3472

East Asian (EAS) AF: 0.993 AC: 5120 AN: 5158

South Asian (SAS) AF: 0.970 AC: 4688 AN: 4834

European-Finnish (FIN) AF: 0.989 AC: 10510 AN: 10630

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.944 AC: 64222 AN: 68018

Other (OTH) AF: 0.906 AC: 1916 AN: 2114

Alfa AF: 0.907 Hom.: 7846

Bravo AF: 0.871

Asia WGS AF: 0.957 AC: 3328 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	0.25
DANN	Benign	0.44
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6509942; hg19: chr19-30554951;