rs7749323

Positions:

• chr6-137909252-G-A

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 0.0333 in 152,234 control chromosomes in the GnomAD database, including 95 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 0.033 (95 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0333 (5070/152234) while in subpopulation AFR AF= 0.0485 (2014/41540). AF 95% confidence interval is 0.0467. There are 95 homozygotes in gnomad4. There are 2426 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 95 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: 0.0333 AC: 5061 AN: 152116 Hom.: 95 Cov.: 32

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0414

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0333 AC: 5070 AN: 152234 Hom.: 95 Cov.: 32 AF XY: 0.0326 AC XY: 2426 AN XY: 74420

Gnomad4 AFR AF: 0.0485

Gnomad4 AMR AF: 0.0240

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.0419

Gnomad4 SAS AF: 0.0363

Gnomad4 FIN AF: 0.0166

Gnomad4 NFE AF: 0.0282

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0316 Hom.: 21

Bravo AF: 0.0338

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7749323; hg19: chr6-138230389;