9-200971-G-T

Variant names:

• chr9-200971-G-T
• rs669980
• ENST00000657756.1:n.180-2202C>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000657756.1(ENSG00000287480):​n.180-2202C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.63 (27760 hom., cov: 17)
• Consequence: ENSG00000287480 ENST00000657756.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 publications found

Genes affected

ENSG00000287480 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS2: High Homozygotes in GnomAd4 at 27760 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657756.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287480	ENST00000657756.1		n.180-2202C>A		intron	N/A
	ENSG00000287480	ENST00000786412.1		n.144+8405C>A		intron	N/A
	ENSG00000287480	ENST00000786413.1		n.118+8405C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.632 AC: 73357 AN: 116096 Hom.: 27688 Cov.: 17

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.553

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.632 AC: 73487 AN: 116198 Hom.: 27760 Cov.: 17 AF XY: 0.627 AC XY: 34917 AN XY: 55674

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.911 AC: 29266 AN: 32114

American (AMR) AF: 0.648 AC: 6669 AN: 10286

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1113 AN: 2722

East Asian (EAS) AF: 0.507 AC: 1522 AN: 3000

South Asian (SAS) AF: 0.579 AC: 1687 AN: 2916

European-Finnish (FIN) AF: 0.496 AC: 4056 AN: 8178

Middle Eastern (MID) AF: 0.560 AC: 130 AN: 232

European-Non Finnish (NFE) AF: 0.510 AC: 27780 AN: 54500

Other (OTH) AF: 0.619 AC: 967 AN: 1562

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.546 Hom.: 1810

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs669980; hg19: chr9-200971; COSMIC: COSV69439712;