7-93418371-C-T

Variant names:

• chr7-93418371-C-T
• rs2374634

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 0.68 in 152,048 control chromosomes in the GnomAD database, including 35,989 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 0.68 (35989 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103330 AN: 151930 Hom.: 35949 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.680 AC: 103428 AN: 152048 Hom.: 35989 Cov.: 32 AF XY: 0.679 AC XY: 50482 AN XY: 74304

African (AFR) AF: 0.791 AC: 32823 AN: 41496

American (AMR) AF: 0.730 AC: 11158 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2394 AN: 3470

East Asian (EAS) AF: 0.889 AC: 4591 AN: 5164

South Asian (SAS) AF: 0.715 AC: 3450 AN: 4826

European-Finnish (FIN) AF: 0.508 AC: 5359 AN: 10544

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.610 AC: 41482 AN: 67950

Other (OTH) AF: 0.709 AC: 1496 AN: 2110

Alfa AF: 0.686 Hom.: 16805

Bravo AF: 0.703

Asia WGS AF: 0.849 AC: 2954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2374634; hg19: chr7-93047683;