rs2778624

Positions:

• chr9-122446782-T-C

Variant summary

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

The ENST00000431442.2(ENSG00000234156):​n.324-647T>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 0.666 in 151,994 control chromosomes in the GnomAD database, including 34,420 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 0.67 (34420 hom., cov: 31)
• Consequence: ENST00000431442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.731 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
	ENST00000431442.2	n.324-647T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000433572.3	n.358-647T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101109 AN: 151876 Hom.: 34404 Cov.: 31

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.666 AC: 101163 AN: 151994 Hom.: 34420 Cov.: 31 AF XY: 0.666 AC XY: 49505 AN XY: 74302

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.659

Alfa AF: 0.717 Hom.: 77393

Bravo AF: 0.653

Asia WGS AF: 0.624 AC: 2169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2778624; hg19: chr9-125209061;