rs7449190

Variant names:

• chr5-1297803-T-C
• rs7449190

Your query was ambiguous. Multiple possible variants found:

• chr5-1297803-T-C
• chr5-1297803-T-G

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 0.88 in 152,118 control chromosomes in the GnomAD database, including 59,149 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 (59149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 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: 0.880 AC: 133775 AN: 152000 Hom.: 59082 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.880 AC: 133903 AN: 152118 Hom.: 59149 Cov.: 32 AF XY: 0.879 AC XY: 65403 AN XY: 74366

African (AFR) AF: 0.949 AC: 39373 AN: 41510

American (AMR) AF: 0.877 AC: 13411 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2758 AN: 3466

East Asian (EAS) AF: 0.874 AC: 4513 AN: 5166

South Asian (SAS) AF: 0.901 AC: 4344 AN: 4820

European-Finnish (FIN) AF: 0.831 AC: 8795 AN: 10584

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57912 AN: 67978

Other (OTH) AF: 0.847 AC: 1783 AN: 2106

Alfa AF: 0.864 Hom.: 7081

Bravo AF: 0.886

Asia WGS AF: 0.908 AC: 3159 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	1.5
DANN	Benign	0.28
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7449190; hg19: chr5-1297918;