5-98419196-G-T

Variant names:

• chr5-98419196-G-T
• rs11241318

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 0.374 in 151,968 control chromosomes in the GnomAD database, including 10,903 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 0.37 (10903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.761
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.374 AC: 56723 AN: 151850 Hom.: 10889 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.374 AC: 56767 AN: 151968 Hom.: 10903 Cov.: 32 AF XY: 0.377 AC XY: 28006 AN XY: 74272

African (AFR) AF: 0.304 AC: 12616 AN: 41454

American (AMR) AF: 0.392 AC: 5987 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1407 AN: 3466

East Asian (EAS) AF: 0.504 AC: 2600 AN: 5160

South Asian (SAS) AF: 0.373 AC: 1801 AN: 4822

European-Finnish (FIN) AF: 0.455 AC: 4801 AN: 10544

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26334 AN: 67950

Other (OTH) AF: 0.394 AC: 831 AN: 2110

Alfa AF: 0.380 Hom.: 6797

Bravo AF: 0.364

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.3
DANN	Benign	0.56
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs11241318; hg19: chr5-97754900;