rs2196311

Positions:

• chr9-121408212-C-A
• chr9-121408212-C-G
• chr9-121408212-C-T

Variant summary

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

The ENST00000658975.1(ENSG00000227355):​n.170-32164C>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 0.739 in 151,908 control chromosomes in the GnomAD database, including 43,300 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 0.74 (43300 hom., cov: 31)
• Consequence: ENST00000658975.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658975.1	n.170-32164C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112211 AN: 151790 Hom.: 43301 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.739 AC: 112235 AN: 151908 Hom.: 43300 Cov.: 31 AF XY: 0.738 AC XY: 54808 AN XY: 74248

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.744

Alfa AF: 0.831 Hom.: 64403

Bravo AF: 0.716

Asia WGS AF: 0.677 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2196311; hg19: chr9-124170490;