rs7752903

chr6-137906227-T-G

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 0.0334 in 152,282 control chromosomes in the GnomAD database, including 98 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 (98 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.598

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0334 (5086/152282) while in subpopulation AFR AF= 0.0485 (2017/41548). AF 95% confidence interval is 0.0468. There are 98 homozygotes in gnomad4. There are 2440 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 98 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: 0.0334 AC: 5077 AN: 152164 Hom.: 98 Cov.: 32

Gnomad AFR AF: 0.0485

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.0370

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0334 AC: 5086 AN: 152282 Hom.: 98 Cov.: 32 AF XY: 0.0328 AC XY: 2440 AN XY: 74466

Gnomad4 AFR AF: 0.0485

Gnomad4 AMR AF: 0.0241

Gnomad4 ASJ AF: 0.0404

Gnomad4 EAS AF: 0.0426

Gnomad4 SAS AF: 0.0366

Gnomad4 FIN AF: 0.0166

Gnomad4 NFE AF: 0.0282

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0330 Hom.: 24

Bravo AF: 0.0338

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	9.0
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7752903; hg19: chr6-138227364;