chr7-19497980-G-C

Variant names:

• chr7-19497980-G-C
• rs10486351
• ENST00000412563.1:n.357-78307G>C

Variant summary

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

The ENST00000412563.1(ENSG00000223838):​n.357-78307G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0967 in 152,066 control chromosomes in the GnomAD database, including 1,437 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 0.097 (1437 hom., cov: 32)
• Consequence: ENSG00000223838 ENST00000412563.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 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.357-78307G>C		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0965 AC: 14666 AN: 151948 Hom.: 1431 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0647

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0859

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

GnomAD4 genome AF: 0.0967 AC: 14706 AN: 152066 Hom.: 1437 Cov.: 32 AF XY: 0.0970 AC XY: 7210 AN XY: 74328

African (AFR) AF: 0.243 AC: 10067 AN: 41400

American (AMR) AF: 0.130 AC: 1992 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0647 AC: 224 AN: 3464

East Asian (EAS) AF: 0.0527 AC: 272 AN: 5164

South Asian (SAS) AF: 0.0570 AC: 275 AN: 4826

European-Finnish (FIN) AF: 0.0167 AC: 177 AN: 10604

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0210 AC: 1430 AN: 68008

Other (OTH) AF: 0.0845 AC: 178 AN: 2106

Alfa AF: 0.0645 Hom.: 106

Bravo AF: 0.109

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.65
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10486351; hg19: chr7-19537603;