chr7-19576899-C-T

Variant names:

• chr7-19576899-C-T
• rs4470914
• ENST00000412563.1:n.488+481C>T

Variant summary

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

The ENST00000412563.1(ENSG00000223838):​n.488+481C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,536 control chromosomes in the GnomAD database, including 4,536 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 0.23 (4536 hom., cov: 32)
• Consequence: ENSG00000223838 ENST00000412563.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.544
• Publications: 35 publications found

Genes affected

ENSG00000223838 (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 (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412563.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223838	ENST00000412563.1	TSL:5	n.488+481C>T		intron	N/A
	ENSG00000223838	ENST00000779058.1		n.231+481C>T		intron	N/A
	ENSG00000223838	ENST00000779059.1		n.190+481C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34452 AN: 151418 Hom.: 4513 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.228 AC: 34516 AN: 151536 Hom.: 4536 Cov.: 32 AF XY: 0.225 AC XY: 16662 AN XY: 74036

African (AFR) AF: 0.359 AC: 14853 AN: 41364

American (AMR) AF: 0.202 AC: 3057 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 670 AN: 3456

East Asian (EAS) AF: 0.203 AC: 1045 AN: 5136

South Asian (SAS) AF: 0.148 AC: 715 AN: 4816

European-Finnish (FIN) AF: 0.131 AC: 1383 AN: 10526

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12048 AN: 67770

Other (OTH) AF: 0.234 AC: 491 AN: 2102

Alfa AF: 0.194 Hom.: 7527

Bravo AF: 0.242

Asia WGS AF: 0.212 AC: 737 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	9.3
DANN	Benign	0.33
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs4470914; hg19: chr7-19616522;