chr7-48778369-T-C

Position:

• chr7-48778369-T-C

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 0.554 in 152,096 control chromosomes in the GnomAD database, including 23,542 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 0.55 (23542 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 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: 0.554 AC: 84230 AN: 151978 Hom.: 23523 Cov.: 33

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.554 AC: 84284 AN: 152096 Hom.: 23542 Cov.: 33 AF XY: 0.558 AC XY: 41475 AN XY: 74332

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.543

Alfa AF: 0.513 Hom.: 19435

Bravo AF: 0.555

Asia WGS AF: 0.563 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.40
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11767191; hg19: chr7-48817965;