7-19576899-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375180	XR_007060245.1	n.128+481C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223838	ENST00000412563.1	n.488+481C>T		intron_variant	Intron 5 of 5	5
ENSG00000223838	ENST00000779058.1	n.231+481C>T		intron_variant	Intron 2 of 4
ENSG00000223838	ENST00000779059.1	n.190+481C>T		intron_variant	Intron 2 of 5

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 v4.3

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;