4-41321175-A-G

Variant names:

• chr4-41321175-A-G
• rs7666149

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.531 AC: 22027 AN: 41488

American (AMR) AF: 0.324 AC: 4951 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1610 AN: 3472

East Asian (EAS) AF: 0.156 AC: 806 AN: 5162

South Asian (SAS) AF: 0.266 AC: 1279 AN: 4816

European-Finnish (FIN) AF: 0.368 AC: 3886 AN: 10566

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.311 AC: 21128 AN: 67982

Other (OTH) AF: 0.374 AC: 789 AN: 2110

Alfa AF: 0.351 Hom.: 1671

Bravo AF: 0.380

Asia WGS AF: 0.233 AC: 811 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.6
DANN	Benign	0.63
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs7666149; hg19: chr4-41323192;