rs7666149

Variant names:

• chr4-41321175-A-G
• rs7666149

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;