chr6-104424941-C-T

Variant names:

• chr6-104424941-C-T
• rs156232

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 0.529 in 152,116 control chromosomes in the GnomAD database, including 24,085 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 0.53 (24085 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

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 = 0.654 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: 0.529 AC: 80394 AN: 151998 Hom.: 24077 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.529 AC: 80423 AN: 152116 Hom.: 24085 Cov.: 32 AF XY: 0.532 AC XY: 39534 AN XY: 74362

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.573

Alfa AF: 0.621 Hom.: 18312

Bravo AF: 0.517

Asia WGS AF: 0.567 AC: 1970 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	3.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs156232; hg19: chr6-104872816;