rs13196614

Variant names:

• chr6-148602653-G-T
• rs13196614

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 0.112 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
• Publications: 7 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0274 AC: 1140 AN: 41544

American (AMR) AF: 0.101 AC: 1544 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0654 AC: 227 AN: 3470

East Asian (EAS) AF: 0.0484 AC: 251 AN: 5182

South Asian (SAS) AF: 0.0529 AC: 255 AN: 4824

European-Finnish (FIN) AF: 0.194 AC: 2044 AN: 10536

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11129 AN: 67986

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.125 Hom.: 457

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs13196614; hg19: chr6-148923789;