rs1349721

Variant names:

• chr4-85415626-T-G
• rs1349721

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 0.377 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.391 AC: 16204 AN: 41480

American (AMR) AF: 0.383 AC: 5851 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3466

East Asian (EAS) AF: 0.231 AC: 1197 AN: 5180

South Asian (SAS) AF: 0.183 AC: 885 AN: 4830

European-Finnish (FIN) AF: 0.374 AC: 3950 AN: 10560

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26875 AN: 67974

Other (OTH) AF: 0.379 AC: 799 AN: 2108

Alfa AF: 0.383 Hom.: 6719

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1349721; hg19: chr4-86336779;