7-46157668-C-T

Variant names:

• chr7-46157668-C-T
• rs11770622

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 0.162 in 152,154 control chromosomes in the GnomAD database, including 2,092 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 0.16 (2092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 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: 0.162 AC: 24562 AN: 152036 Hom.: 2085 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.162 AC: 24584 AN: 152154 Hom.: 2092 Cov.: 32 AF XY: 0.161 AC XY: 11968 AN XY: 74378

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.154

Alfa AF: 0.167 Hom.: 1697

Bravo AF: 0.154

Asia WGS AF: 0.226 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11770622; hg19: chr7-46197266;