rs7669317

Positions:

• chr4-105536173-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.029 in 152,296 control chromosomes in the GnomAD database, including 86 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 0.029 (86 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.029 (4421/152296) while in subpopulation NFE AF= 0.0393 (2669/67984). AF 95% confidence interval is 0.038. There are 86 homozygotes in gnomad4. There are 2103 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 86 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0290 AC: 4419 AN: 152178 Hom.: 86 Cov.: 32

Gnomad AFR AF: 0.00748

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0393

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0290 AC: 4421 AN: 152296 Hom.: 86 Cov.: 32 AF XY: 0.0282 AC XY: 2103 AN XY: 74472

Gnomad4 AFR AF: 0.00748

Gnomad4 AMR AF: 0.0332

Gnomad4 ASJ AF: 0.0980

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0157

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0393

Gnomad4 OTH AF: 0.0312

Alfa AF: 0.0392 Hom.: 147

Bravo AF: 0.0280

Asia WGS AF: 0.00751 AC: 27 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7669317; hg19: chr4-106457330;