rs7249702

Variant names:

• chr19-14027400-G-A
• rs7249702

Your query was ambiguous. Multiple possible variants found:

• chr19-14027400-G-A
• chr19-14027400-G-T

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 0.322 in 151,922 control chromosomes in the GnomAD database, including 10,930 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 0.32 (10930 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.811
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 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: 0.322 AC: 48907 AN: 151804 Hom.: 10896 Cov.: 30

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.322 AC: 48992 AN: 151922 Hom.: 10930 Cov.: 30 AF XY: 0.322 AC XY: 23890 AN XY: 74254

African (AFR) AF: 0.627 AC: 25955 AN: 41398

American (AMR) AF: 0.236 AC: 3598 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3472

East Asian (EAS) AF: 0.398 AC: 2050 AN: 5150

South Asian (SAS) AF: 0.367 AC: 1762 AN: 4806

European-Finnish (FIN) AF: 0.174 AC: 1839 AN: 10556

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12552 AN: 67976

Other (OTH) AF: 0.277 AC: 585 AN: 2110

Alfa AF: 0.227 Hom.: 6308

Bravo AF: 0.338

Asia WGS AF: 0.403 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.84
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs7249702; hg19: chr19-14138212;