rs7661864

Positions:

• chr4-6734638-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 0.355 in 152,016 control chromosomes in the GnomAD database, including 10,229 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 0.35 (10229 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

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 (AFR) allele frequency at 95% confidence interval = 0.502 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: 0.355 AC: 53906 AN: 151898 Hom.: 10214 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.355 AC: 53960 AN: 152016 Hom.: 10229 Cov.: 32 AF XY: 0.348 AC XY: 25862 AN XY: 74292

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.355

Alfa AF: 0.312 Hom.: 7714

Bravo AF: 0.370

Asia WGS AF: 0.326 AC: 1139 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	0.98
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7661864; hg19: chr4-6736365;