7-106506823-G-C

Variant names:

• chr7-106506823-G-C
• rs10486020
• ENST00000485282.5:n.312-15693C>G

Variant summary

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

The ENST00000485282.5(ENSG00000243797):​n.312-15693C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,136 control chromosomes in the GnomAD database, including 7,919 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 0.31 (7919 hom., cov: 32)
• Consequence: ENSG00000243797 ENST00000485282.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 2 publications found

Genes affected

ENSG00000243797 (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 (AMR) allele frequency at 95% confidence interval = 0.421 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
ENSG00000243797	ENST00000485282.5	n.312-15693C>G		intron_variant	Intron 3 of 4	3
ENSG00000243797	ENST00000490856.5	n.266+13906C>G		intron_variant	Intron 3 of 4	4
ENSG00000243797	ENST00000592441.1	n.240-15693C>G		intron_variant	Intron 3 of 4	2

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46411 AN: 152018 Hom.: 7920 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.305 AC: 46423 AN: 152136 Hom.: 7919 Cov.: 32 AF XY: 0.305 AC XY: 22716 AN XY: 74370

African (AFR) AF: 0.169 AC: 7033 AN: 41514

American (AMR) AF: 0.430 AC: 6563 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3472

East Asian (EAS) AF: 0.132 AC: 686 AN: 5184

South Asian (SAS) AF: 0.295 AC: 1423 AN: 4824

European-Finnish (FIN) AF: 0.300 AC: 3172 AN: 10560

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.367 AC: 24969 AN: 67986

Other (OTH) AF: 0.333 AC: 705 AN: 2114

Alfa AF: 0.187 Hom.: 383

Bravo AF: 0.308

Asia WGS AF: 0.215 AC: 749 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	2.4
DANN	Benign	0.56
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10486020; hg19: chr7-106147269;