rs7658327

Positions:

• chr4-135190295-C-A
• chr4-135190295-C-G

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 0.661 in 151,810 control chromosomes in the GnomAD database, including 33,581 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 0.66 (33581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

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 = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100241 AN: 151692 Hom.: 33549 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.661 AC: 100328 AN: 151810 Hom.: 33581 Cov.: 32 AF XY: 0.667 AC XY: 49476 AN XY: 74204

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.681

Alfa AF: 0.671 Hom.: 44264

Bravo AF: 0.660

Asia WGS AF: 0.730 AC: 2522 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.9
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7658327; hg19: chr4-136111450;