rs13196614

Positions:

• chr6-148602653-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 0.112 in 152,156 control chromosomes in the GnomAD database, including 1,269 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 0.11 (1269 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

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: 0.112 AC: 17001 AN: 152038 Hom.: 1267 Cov.: 33

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0654

Gnomad EAS AF: 0.0487

Gnomad SAS AF: 0.0528

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.112 AC: 16996 AN: 152156 Hom.: 1269 Cov.: 33 AF XY: 0.110 AC XY: 8206 AN XY: 74370

Gnomad4 AFR AF: 0.0274

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0654

Gnomad4 EAS AF: 0.0484

Gnomad4 SAS AF: 0.0529

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.118

Alfa AF: 0.132 Hom.: 256

Bravo AF: 0.0991

Asia WGS AF: 0.0450 AC: 155 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13196614; hg19: chr6-148923789;