rs7220740

Positions:

• chr17-61663432-C-A
• chr17-61663432-C-G
• chr17-61663432-C-T

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 0.292 in 151,982 control chromosomes in the GnomAD database, including 6,689 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 0.29 (6689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44370 AN: 151864 Hom.: 6680 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.292 AC: 44409 AN: 151982 Hom.: 6689 Cov.: 32 AF XY: 0.290 AC XY: 21574 AN XY: 74302

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.301

Alfa AF: 0.267 Hom.: 3252

Bravo AF: 0.297

Asia WGS AF: 0.320 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.62
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7220740; hg19: chr17-59740793;