rs223019

Variant names:

• chr7-74161268-T-C
• rs223019
• ENST00000779783.1:n.458+12324A>G

Variant summary

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

The ENST00000779783.1(ENSG00000301571):​n.458+12324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 150,116 control chromosomes in the GnomAD database, including 29,123 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 0.62 (29123 hom., cov: 26)
• Consequence: ENSG00000301571 ENST00000779783.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86
• Publications: 6 publications found

Genes affected

ENSG00000301571 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779783.1. 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
	ENSG00000301571	ENST00000779783.1		n.458+12324A>G		intron	N/A
	ENSG00000301571	ENST00000779787.1		n.432+12312A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.622 AC: 93234 AN: 149998 Hom.: 29101 Cov.: 26

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.621 AC: 93297 AN: 150116 Hom.: 29123 Cov.: 26 AF XY: 0.623 AC XY: 45609 AN XY: 73206

African (AFR) AF: 0.571 AC: 23350 AN: 40902

American (AMR) AF: 0.616 AC: 9272 AN: 15042

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2155 AN: 3462

East Asian (EAS) AF: 0.748 AC: 3698 AN: 4946

South Asian (SAS) AF: 0.582 AC: 2739 AN: 4704

European-Finnish (FIN) AF: 0.674 AC: 7009 AN: 10406

Middle Eastern (MID) AF: 0.729 AC: 210 AN: 288

European-Non Finnish (NFE) AF: 0.639 AC: 43077 AN: 67374

Other (OTH) AF: 0.631 AC: 1323 AN: 2096

Alfa AF: 0.619 Hom.: 3231

Bravo AF: 0.621

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.34
DANN	Benign	0.33
PhyloP100		-2.9

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: rs223019;

hg19: chr7-73575598;