chr5-19440059-T-C

Variant names:

• chr5-19440059-T-C
• rs349475

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 0.635 in 151,976 control chromosomes in the GnomAD database, including 30,746 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 0.63 (30746 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.663 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: 0.635 AC: 96383 AN: 151858 Hom.: 30733 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.635 AC: 96438 AN: 151976 Hom.: 30746 Cov.: 31 AF XY: 0.634 AC XY: 47088 AN XY: 74304

African (AFR) AF: 0.631 AC: 26161 AN: 41460

American (AMR) AF: 0.550 AC: 8402 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2282 AN: 3468

East Asian (EAS) AF: 0.600 AC: 3093 AN: 5154

South Asian (SAS) AF: 0.682 AC: 3290 AN: 4824

European-Finnish (FIN) AF: 0.685 AC: 7230 AN: 10558

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.646 AC: 43871 AN: 67938

Other (OTH) AF: 0.640 AC: 1349 AN: 2108

Alfa AF: 0.641 Hom.: 122692

Bravo AF: 0.624

Asia WGS AF: 0.666 AC: 2320 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	0.46
DANN	Benign	0.80
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs349475; hg19: chr5-19440168;