rs7658637

chr4-82578160-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 0.0249 in 152,294 control chromosomes in the GnomAD database, including 127 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 0.025 (127 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0619 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: 0.0249 AC: 3793 AN: 152176 Hom.: 127 Cov.: 33

Gnomad AFR AF: 0.0640

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0207

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.000659

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00473

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0249 AC: 3799 AN: 152294 Hom.: 127 Cov.: 33 AF XY: 0.0248 AC XY: 1849 AN XY: 74474

Gnomad4 AFR AF: 0.0639

Gnomad4 AMR AF: 0.0206

Gnomad4 ASJ AF: 0.0184

Gnomad4 EAS AF: 0.0342

Gnomad4 SAS AF: 0.0406

Gnomad4 FIN AF: 0.000659

Gnomad4 NFE AF: 0.00473

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.00979 Hom.: 25

Bravo AF: 0.0278

Asia WGS AF: 0.0250 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	7.1
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7658637; hg19: chr4-83499313;