chr7-51470190-C-T

Variant names:

• chr7-51470190-C-T
• rs1949829

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 0.12 in 152,194 control chromosomes in the GnomAD database, including 1,631 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 0.12 (1631 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272

ACMG classification

Verdict is Benign. Variant got -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 = 0.236 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: 0.120 AC: 18270 AN: 152076 Hom.: 1625 Cov.: 34

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0601

Gnomad OTH AF: 0.0998

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

GnomAD4 genome AF: 0.120 AC: 18305 AN: 152194 Hom.: 1631 Cov.: 34 AF XY: 0.120 AC XY: 8938 AN XY: 74396

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0578

Gnomad4 NFE AF: 0.0601

Gnomad4 OTH AF: 0.0997

Alfa AF: 0.0716 Hom.: 1038

Bravo AF: 0.131

Asia WGS AF: 0.180 AC: 624 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	3.1
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1949829; hg19: chr7-51537887;