rs13204742

chr6-127924620-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0923 in 152,208 control chromosomes in the GnomAD database, including 776 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 0.092 (776 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

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: 0.0924 AC: 14051 AN: 152090 Hom.: 778 Cov.: 32

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0719

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0901

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.0855

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

GnomAD4 genome AF: 0.0923 AC: 14044 AN: 152208 Hom.: 776 Cov.: 32 AF XY: 0.0901 AC XY: 6705 AN XY: 74408

Gnomad4 AFR AF: 0.0411

Gnomad4 AMR AF: 0.0718

Gnomad4 ASJ AF: 0.0781

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0893

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.0846

Alfa AF: 0.104 Hom.: 205

Bravo AF: 0.0828

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13204742; hg19: chr6-128245765;