rs7219249

Variant names:

• chr17-41676424-G-A
• rs7219249

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 0.495 in 151,968 control chromosomes in the GnomAD database, including 19,096 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 0.49 (19096 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.647 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: 0.495 AC: 75145 AN: 151850 Hom.: 19074 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.495 AC: 75201 AN: 151968 Hom.: 19096 Cov.: 32 AF XY: 0.504 AC XY: 37464 AN XY: 74262

African (AFR) AF: 0.376 AC: 15583 AN: 41434

American (AMR) AF: 0.534 AC: 8142 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2994 AN: 5160

South Asian (SAS) AF: 0.666 AC: 3209 AN: 4818

European-Finnish (FIN) AF: 0.625 AC: 6600 AN: 10562

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35340 AN: 67952

Other (OTH) AF: 0.504 AC: 1063 AN: 2110

Alfa AF: 0.498 Hom.: 25194

Bravo AF: 0.477

Asia WGS AF: 0.611 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.57
DANN	Benign	0.32
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7219249; hg19: chr17-39832676;