7-107239-G-C

Variant names:

• chr7-107239-G-C
• rs6583343
• ENST00000821340.1:n.419+10669C>G

Variant summary

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

The ENST00000821340.1(ENSG00000287883):​n.419+10669C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,930 control chromosomes in the GnomAD database, including 14,493 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 0.43 (14493 hom., cov: 32)
• Consequence: ENSG00000287883 ENST00000821340.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 2 publications found

Genes affected

ENSG00000287883 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287883	ENST00000821340.1	n.419+10669C>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64899 AN: 151812 Hom.: 14482 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.427 AC: 64931 AN: 151930 Hom.: 14493 Cov.: 32 AF XY: 0.429 AC XY: 31891 AN XY: 74256

African (AFR) AF: 0.370 AC: 15316 AN: 41394

American (AMR) AF: 0.382 AC: 5846 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1493 AN: 3466

East Asian (EAS) AF: 0.840 AC: 4335 AN: 5162

South Asian (SAS) AF: 0.497 AC: 2390 AN: 4806

European-Finnish (FIN) AF: 0.416 AC: 4391 AN: 10552

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29624 AN: 67952

Other (OTH) AF: 0.467 AC: 986 AN: 2110

Alfa AF: 0.257 Hom.: 562

Bravo AF: 0.427

Asia WGS AF: 0.663 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.21
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6583343; hg19: chr7-107239;