rs6849561

chr4-119488539-G-C

Variant summary

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

The NR_037630.1(SEPTIN7P14):n.728-4794G>C 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 0.266 in 151,902 control chromosomes in the GnomAD database, including 5,471 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 0.27 (5469 hom., cov: 32)
  • Exomes 𝑓: 0.30 (2 hom.)
• Consequence: SEPTIN7P14 NR_037630.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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	UniProt
SEPTIN7P14	NR_037630.1	n.728-4794G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000688315.1	n.715-4794G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40308 AN: 151732 Hom.: 5464 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.280

GnomAD4 exome AF: 0.300 AC: 15 AN: 50 Hom.: 2 AF XY: 0.206 AC XY: 7 AN XY: 34

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.286

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.266 AC: 40343 AN: 151852 Hom.: 5469 Cov.: 32 AF XY: 0.264 AC XY: 19565 AN XY: 74216

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.278

Alfa AF: 0.268 Hom.: 719

Bravo AF: 0.271

Asia WGS AF: 0.251 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.23
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6849561; hg19: chr4-120409694;