rs9320913

chr6-98136857-C-A

Variant summary

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

The ENST00000656098.1(ENSG00000271860):n.1400+37587C>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 0.384 in 148,960 control chromosomes in the GnomAD database, including 11,815 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 (11815 hom., cov: 31)
• Consequence: ENST00000656098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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
	ENST00000656098.1	n.1400+37587C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.384 AC: 57219 AN: 148856 Hom.: 11819 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.384 AC: 57208 AN: 148960 Hom.: 11815 Cov.: 31 AF XY: 0.381 AC XY: 27726 AN XY: 72688

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.387

Alfa AF: 0.00809 Hom.: 17

Bravo AF: 0.371

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.37
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9320913; hg19: chr6-98584733;