rs13204742

Variant names:

• chr6-127924620-G-T
• rs13204742

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0411 AC: 1709 AN: 41532

American (AMR) AF: 0.0718 AC: 1097 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0893 AC: 431 AN: 4824

European-Finnish (FIN) AF: 0.127 AC: 1341 AN: 10592

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8937 AN: 68002

Other (OTH) AF: 0.0846 AC: 179 AN: 2116

Alfa AF: 0.109 Hom.: 1628

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs13204742; hg19: chr6-128245765;