7-96776068-G-T

Variant names:

• chr7-96776068-G-T
• rs17499178

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 0.0398 in 152,058 control chromosomes in the GnomAD database, including 178 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 0.040 (178 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.0579 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: 0.0399 AC: 6060 AN: 151940 Hom.: 178 Cov.: 31

Gnomad AFR AF: 0.00952

Gnomad AMI AF: 0.0441

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0322

Gnomad FIN AF: 0.0565

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0594

Gnomad OTH AF: 0.0432

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

GnomAD4 genome AF: 0.0398 AC: 6056 AN: 152058 Hom.: 178 Cov.: 31 AF XY: 0.0395 AC XY: 2934 AN XY: 74336

African (AFR) AF: 0.00950 AC: 394 AN: 41490

American (AMR) AF: 0.0323 AC: 494 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3466

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5154

South Asian (SAS) AF: 0.0318 AC: 153 AN: 4816

European-Finnish (FIN) AF: 0.0565 AC: 597 AN: 10568

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0595 AC: 4042 AN: 67972

Other (OTH) AF: 0.0428 AC: 90 AN: 2104

Alfa AF: 0.0331 Hom.: 58

Bravo AF: 0.0364

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.27
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs17499178; hg19: chr7-96405380;