rs17664743

Positions:

• chr7-50214301-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.239 in 152,184 control chromosomes in the GnomAD database, including 5,063 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 0.24 (5063 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50214301G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231681	ENST00000639870.1	n.215-10235C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36381 AN: 152066 Hom.: 5064 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.239 AC: 36406 AN: 152184 Hom.: 5063 Cov.: 33 AF XY: 0.239 AC XY: 17777 AN XY: 74406

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.284

Alfa AF: 0.221 Hom.: 1056

Bravo AF: 0.253

Asia WGS AF: 0.317 AC: 1102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.62
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17664743; hg19: chr7-50253897;