7-119966578-C-T

Position:

• chr7-119966578-C-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 0.0527 in 152,132 control chromosomes in the GnomAD database, including 494 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 0.053 (494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

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 (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0526 AC: 7997 AN: 152014 Hom.: 490 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0408

Gnomad ASJ AF: 0.0214

Gnomad EAS AF: 0.0531

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.00679

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00907

Gnomad OTH AF: 0.0475

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

GnomAD4 genome AF: 0.0527 AC: 8012 AN: 152132 Hom.: 494 Cov.: 32 AF XY: 0.0513 AC XY: 3814 AN XY: 74382

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0407

Gnomad4 ASJ AF: 0.0214

Gnomad4 EAS AF: 0.0528

Gnomad4 SAS AF: 0.0476

Gnomad4 FIN AF: 0.00679

Gnomad4 NFE AF: 0.00907

Gnomad4 OTH AF: 0.0480

Alfa AF: 0.0155 Hom.: 65

Bravo AF: 0.0593

Asia WGS AF: 0.0610 AC: 210 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	0.29
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17142462; hg19: chr7-119606632;