rs7666149

chr4-41321175-A-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 0.375 in 152,078 control chromosomes in the GnomAD database, including 11,565 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 0.38 (11565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 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: 0.375 AC: 56934 AN: 151962 Hom.: 11521 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.375 AC: 57030 AN: 152078 Hom.: 11565 Cov.: 32 AF XY: 0.374 AC XY: 27783 AN XY: 74320

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.374

Alfa AF: 0.345 Hom.: 1566

Bravo AF: 0.380

Asia WGS AF: 0.233 AC: 811 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	9.6
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7666149; hg19: chr4-41323192;