rs7249990

Variant names:

• chr19-34687938-T-C
• rs7249990

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 0.298 in 152,072 control chromosomes in the GnomAD database, including 7,535 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 0.30 (7535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.364 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: 0.298 AC: 45315 AN: 151954 Hom.: 7540 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.298 AC: 45311 AN: 152072 Hom.: 7535 Cov.: 32 AF XY: 0.298 AC XY: 22172 AN XY: 74324

African (AFR) AF: 0.163 AC: 6778 AN: 41504

American (AMR) AF: 0.274 AC: 4197 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1222 AN: 3466

East Asian (EAS) AF: 0.273 AC: 1403 AN: 5144

South Asian (SAS) AF: 0.257 AC: 1240 AN: 4822

European-Finnish (FIN) AF: 0.396 AC: 4180 AN: 10562

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25016 AN: 67968

Other (OTH) AF: 0.304 AC: 643 AN: 2112

Alfa AF: 0.327 Hom.: 1124

Bravo AF: 0.281

Asia WGS AF: 0.262 AC: 909 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	8.7
DANN	Benign	0.36
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs7249990; hg19: chr19-35178843;