19-41856664-C-G

Variant names:

• chr19-41856664-C-G
• rs7258162

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 0.257 in 152,112 control chromosomes in the GnomAD database, including 6,089 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 0.26 (6089 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.374 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: 0.257 AC: 39107 AN: 151992 Hom.: 6089 Cov.: 31

Gnomad AFR AF: 0.0849

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.257 AC: 39102 AN: 152112 Hom.: 6089 Cov.: 31 AF XY: 0.261 AC XY: 19401 AN XY: 74360

African (AFR) AF: 0.0847 AC: 3516 AN: 41518

American (AMR) AF: 0.344 AC: 5252 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1414 AN: 3472

East Asian (EAS) AF: 0.184 AC: 950 AN: 5168

South Asian (SAS) AF: 0.389 AC: 1875 AN: 4826

European-Finnish (FIN) AF: 0.291 AC: 3073 AN: 10552

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21920 AN: 67982

Other (OTH) AF: 0.296 AC: 626 AN: 2112

Alfa AF: 0.280 Hom.: 831

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs7258162; hg19: chr19-42360735;