rs4422679

Variant names:

• chr7-11910321-A-G
• rs4422679
• ENST00000775347.1:n.291-3879T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-11910321-A-G
• chr7-11910321-A-T

Variant summary

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

The ENST00000775347.1(ENSG00000300984):​n.291-3879T>C 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 152,094 control chromosomes in the GnomAD database, including 15,017 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 (15017 hom., cov: 32)
• Consequence: ENSG00000300984 ENST00000775347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 1 publications found

Genes affected

ENSG00000300984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775347.1. 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
	ENSG00000300984	ENST00000775347.1		n.291-3879T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64808 AN: 151976 Hom.: 14987 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.427 AC: 64899 AN: 152094 Hom.: 15017 Cov.: 32 AF XY: 0.428 AC XY: 31845 AN XY: 74340

African (AFR) AF: 0.565 AC: 23415 AN: 41472

American (AMR) AF: 0.452 AC: 6906 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1497 AN: 3470

East Asian (EAS) AF: 0.727 AC: 3744 AN: 5150

South Asian (SAS) AF: 0.395 AC: 1904 AN: 4826

European-Finnish (FIN) AF: 0.324 AC: 3430 AN: 10600

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22704 AN: 67980

Other (OTH) AF: 0.406 AC: 855 AN: 2104

Alfa AF: 0.409 Hom.: 2215

Bravo AF: 0.446

Asia WGS AF: 0.544 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.3
DANN	Benign	0.83
PhyloP100		1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4422679;

hg19: chr7-11949947;