7-19571684-G-T

Variant names:

• chr7-19571684-G-T
• rs10230207
• ENST00000412563.1:n.357-4603G>T

Variant summary

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

The ENST00000412563.1(ENSG00000223838):​n.357-4603G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,860 control chromosomes in the GnomAD database, including 21,048 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 0.49 (21048 hom., cov: 32)
• Consequence: ENSG00000223838 ENST00000412563.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 11 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 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
ENSG00000223838	ENST00000412563.1	n.357-4603G>T		intron_variant	Intron 4 of 5	5
ENSG00000223838	ENST00000779060.1	n.83-6845G>T		intron_variant	Intron 1 of 1
ENSG00000223838	ENST00000779061.1	n.237-6845G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74600 AN: 151742 Hom.: 21039 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.491 AC: 74634 AN: 151860 Hom.: 21048 Cov.: 32 AF XY: 0.487 AC XY: 36136 AN XY: 74204

African (AFR) AF: 0.250 AC: 10345 AN: 41430

American (AMR) AF: 0.464 AC: 7072 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1041 AN: 5160

South Asian (SAS) AF: 0.335 AC: 1612 AN: 4812

European-Finnish (FIN) AF: 0.714 AC: 7538 AN: 10562

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43145 AN: 67866

Other (OTH) AF: 0.505 AC: 1066 AN: 2112

Alfa AF: 0.579 Hom.: 36067

Bravo AF: 0.465

Asia WGS AF: 0.276 AC: 960 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.29
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs10230207; hg19: chr7-19611307;