7-48778369-T-C

Variant names:

• chr7-48778369-T-C
• rs11767191

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 0.554 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.606 AC: 25157 AN: 41482

American (AMR) AF: 0.561 AC: 8572 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1745 AN: 3466

East Asian (EAS) AF: 0.643 AC: 3320 AN: 5166

South Asian (SAS) AF: 0.573 AC: 2763 AN: 4824

European-Finnish (FIN) AF: 0.568 AC: 6008 AN: 10570

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35033 AN: 67990

Other (OTH) AF: 0.543 AC: 1145 AN: 2110

Alfa AF: 0.525 Hom.: 29749

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
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs11767191; hg19: chr7-48817965;