rs7665590

chr4-98875633-T-C

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 0.559 in 151,368 control chromosomes in the GnomAD database, including 26,076 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 0.56 (26076 hom., cov: 30)
  • Exomes 𝑓: 0.28 (6 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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: 0.559 AC: 84490 AN: 151248 Hom.: 26012 Cov.: 30

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.552

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.277 AC: 26 AN: 94 Hom.: 6 Cov.: 0 AF XY: 0.256 AC XY: 20 AN XY: 78

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.256

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.559 AC: 84622 AN: 151368 Hom.: 26076 Cov.: 30 AF XY: 0.555 AC XY: 41029 AN XY: 73924

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.552

Alfa AF: 0.496 Hom.: 2584

Bravo AF: 0.581

Asia WGS AF: 0.525 AC: 1831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.11

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7665590; hg19: chr4-99796784;