chr7-99795295-C-CACA

Position:

• chr7-99795295-C-CACA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The variant allele was found at a frequency of 0.0235 in 152,254 control chromosomes in the GnomAD database, including 69 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.024 (69 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0235 (3580/152254) while in subpopulation SAS AF= 0.0521 (251/4818). AF 95% confidence interval is 0.0468. There are 69 homozygotes in gnomad4. There are 1783 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 69 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0235 AC: 3578 AN: 152136 Hom.: 69 Cov.: 31

Gnomad AFR AF: 0.00444

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0235 AC: 3580 AN: 152254 Hom.: 69 Cov.: 31 AF XY: 0.0240 AC XY: 1783 AN XY: 74430

Gnomad4 AFR AF: 0.00443

Gnomad4 AMR AF: 0.0240

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0521

Gnomad4 FIN AF: 0.0222

Gnomad4 NFE AF: 0.0339

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0287 Hom.: 4

Bravo AF: 0.0213

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34401238; hg19: chr7-99392918;