rs1456696

Variant names:

• chr6-122189741-C-T
• rs1456696

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 0.235 in 152,160 control chromosomes in the GnomAD database, including 4,848 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 0.24 (4848 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 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: 0.236 AC: 35833 AN: 152040 Hom.: 4847 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.235 AC: 35825 AN: 152160 Hom.: 4848 Cov.: 32 AF XY: 0.231 AC XY: 17151 AN XY: 74376

African (AFR) AF: 0.109 AC: 4524 AN: 41528

American (AMR) AF: 0.225 AC: 3440 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3464

East Asian (EAS) AF: 0.363 AC: 1876 AN: 5170

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4822

European-Finnish (FIN) AF: 0.213 AC: 2255 AN: 10572

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20504 AN: 68000

Other (OTH) AF: 0.250 AC: 527 AN: 2110

Alfa AF: 0.264 Hom.: 711

Bravo AF: 0.236

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.91
DANN	Benign	0.77
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1456696; hg19: chr6-122510887;