4-119468877-A-G

Position:

• chr4-119468877-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_037630.1(SEPTIN7P14):​n.727+5898A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,012 control chromosomes in the GnomAD database, including 5,834 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 0.28 (5834 hom., cov: 32)
• Consequence: SEPTIN7P14 NR_037630.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEPTIN7P14	NR_037630.1	n.727+5898A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000688315.1	n.714+5898A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41840 AN: 151894 Hom.: 5826 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.276 AC: 41882 AN: 152012 Hom.: 5834 Cov.: 32 AF XY: 0.273 AC XY: 20280 AN XY: 74320

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.282

Alfa AF: 0.282 Hom.: 7620

Bravo AF: 0.283

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11098524; hg19: chr4-120390032;