6-137922563-G-A

Position:

• chr6-137922563-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 0.0264 in 152,118 control chromosomes in the GnomAD database, including 54 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 0.026 (54 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0264 (4014/152118) while in subpopulation SAS AF= 0.0332 (160/4822). AF 95% confidence interval is 0.029. There are 54 homozygotes in gnomad4. There are 1895 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 54 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: 0.0264 AC: 4011 AN: 152000 Hom.: 54 Cov.: 32

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0273

Gnomad SAS AF: 0.0334

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0210

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

GnomAD4 genome AF: 0.0264 AC: 4014 AN: 152118 Hom.: 54 Cov.: 32 AF XY: 0.0255 AC XY: 1895 AN XY: 74392

Gnomad4 AFR AF: 0.0242

Gnomad4 AMR AF: 0.0229

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.0274

Gnomad4 SAS AF: 0.0332

Gnomad4 FIN AF: 0.0167

Gnomad4 NFE AF: 0.0292

Gnomad4 OTH AF: 0.0218

Alfa AF: 0.0287 Hom.: 11

Bravo AF: 0.0256

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61117627; hg19: chr6-138243700;