7-21203899-T-C

Variant names:

• chr7-21203899-T-C
• rs11761356
• ENST00000842806.1:n.173-3027T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000842806.1(ENSG00000309656):​n.173-3027T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 150,350 control chromosomes in the GnomAD database, including 30,263 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 0.61 (30263 hom., cov: 27)
• Consequence: ENSG00000309656 ENST00000842806.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 3 publications found

Genes affected

ENSG00000309656 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842806.1. 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
	ENSG00000309656	ENST00000842806.1		n.173-3027T>C		intron	N/A
	ENSG00000309656	ENST00000842807.1		n.160-4336T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.610 AC: 91572 AN: 150234 Hom.: 30258 Cov.: 27

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.609 AC: 91601 AN: 150350 Hom.: 30263 Cov.: 27 AF XY: 0.611 AC XY: 44733 AN XY: 73204

African (AFR) AF: 0.340 AC: 13942 AN: 40978

American (AMR) AF: 0.656 AC: 9882 AN: 15062

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2678 AN: 3458

East Asian (EAS) AF: 0.576 AC: 2917 AN: 5068

South Asian (SAS) AF: 0.575 AC: 2702 AN: 4700

European-Finnish (FIN) AF: 0.720 AC: 7260 AN: 10078

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.738 AC: 49999 AN: 67720

Other (OTH) AF: 0.650 AC: 1355 AN: 2086

Alfa AF: 0.687 Hom.: 97500

Bravo AF: 0.593

Asia WGS AF: 0.574 AC: 1998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.8
DANN	Benign	0.88
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs11761356; hg19: chr7-21243518;