7-51938719-T-C

Variant names:

• chr7-51938719-T-C
• rs406001

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 0.939 in 152,156 control chromosomes in the GnomAD database, including 67,487 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 0.94 (67487 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142767 AN: 152038 Hom.: 67440 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.963

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.920

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.948

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

GnomAD4 genome AF: 0.939 AC: 142869 AN: 152156 Hom.: 67487 Cov.: 31 AF XY: 0.940 AC XY: 69959 AN XY: 74412

African (AFR) AF: 0.823 AC: 34130 AN: 41478

American (AMR) AF: 0.956 AC: 14608 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3419 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5142 AN: 5154

South Asian (SAS) AF: 0.963 AC: 4641 AN: 4820

European-Finnish (FIN) AF: 0.998 AC: 10590 AN: 10610

Middle Eastern (MID) AF: 0.925 AC: 270 AN: 292

European-Non Finnish (NFE) AF: 0.988 AC: 67232 AN: 68020

Other (OTH) AF: 0.948 AC: 2005 AN: 2114

Alfa AF: 0.973 Hom.: 268342

Bravo AF: 0.931

Asia WGS AF: 0.973 AC: 3383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs406001; hg19: chr7-52006415;