rs4605275

Variant names:

• chr19-44835236-T-C
• rs4605275

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 0.686 in 151,650 control chromosomes in the GnomAD database, including 35,923 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 0.69 (35923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 17 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 (AMR) allele frequency at 95% confidence interval = 0.765 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: 0.686 AC: 103897 AN: 151538 Hom.: 35888 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.686 AC: 103974 AN: 151650 Hom.: 35923 Cov.: 32 AF XY: 0.688 AC XY: 50964 AN XY: 74074

African (AFR) AF: 0.652 AC: 26950 AN: 41356

American (AMR) AF: 0.777 AC: 11809 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2386 AN: 3468

East Asian (EAS) AF: 0.385 AC: 1988 AN: 5166

South Asian (SAS) AF: 0.627 AC: 3022 AN: 4820

European-Finnish (FIN) AF: 0.748 AC: 7826 AN: 10460

Middle Eastern (MID) AF: 0.745 AC: 216 AN: 290

European-Non Finnish (NFE) AF: 0.702 AC: 47687 AN: 67888

Other (OTH) AF: 0.688 AC: 1439 AN: 2092

Alfa AF: 0.696 Hom.: 4563

Bravo AF: 0.687

Asia WGS AF: 0.529 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.18
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4605275; hg19: chr19-45338493;