rs1349721

Positions:

• chr4-85415626-T-G

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 0.377 in 152,090 control chromosomes in the GnomAD database, including 11,141 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 0.38 (11141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57296 AN: 151972 Hom.: 11114 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.377 AC: 57371 AN: 152090 Hom.: 11141 Cov.: 32 AF XY: 0.372 AC XY: 27686 AN XY: 74358

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.379

Alfa AF: 0.387 Hom.: 3304

Bravo AF: 0.383

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1349721; hg19: chr4-86336779;