rs1930713

chr9-117971434-G-A

Variant summary

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

The ENST00000697639.1(ENSG00000284977):n.1054-85596G>A 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 0.228 in 152,194 control chromosomes in the GnomAD database, including 4,217 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 0.23 (4217 hom., cov: 33)
• Consequence: ENST00000697639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000697639.1	n.1054-85596G>A		intron_variant, non_coding_transcript_variant
	ENST00000697724.1	n.1173-85596G>A		intron_variant, non_coding_transcript_variant
	ENST00000703416.1	n.347-85596G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34731 AN: 152076 Hom.: 4211 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.228 AC: 34758 AN: 152194 Hom.: 4217 Cov.: 33 AF XY: 0.226 AC XY: 16789 AN XY: 74422

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.0383

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.246

Alfa AF: 0.245 Hom.: 9659

Bravo AF: 0.227

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1930713; hg19: chr9-120733712;