7-106625119-C-G

Variant names:

• chr7-106625119-C-G
• rs41835
• ENST00000485282.5:n.150-9348G>C

Variant summary

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

The ENST00000592441.1(ENSG00000243797):​n.173-14656G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 151,946 control chromosomes in the GnomAD database, including 38,270 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 0.71 (38270 hom., cov: 31)
• Consequence: ENSG00000243797 ENST00000592441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592441.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243797	ENST00000485282.5	TSL:3	n.150-9348G>C		intron	N/A
	ENSG00000243797	ENST00000490856.5	TSL:4	n.109-14656G>C		intron	N/A
	ENSG00000243797	ENST00000592441.1	TSL:2	n.173-14656G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107405 AN: 151828 Hom.: 38221 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.708 AC: 107516 AN: 151946 Hom.: 38270 Cov.: 31 AF XY: 0.706 AC XY: 52370 AN XY: 74222

African (AFR) AF: 0.754 AC: 31251 AN: 41456

American (AMR) AF: 0.700 AC: 10671 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2235 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2413 AN: 5150

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4814

European-Finnish (FIN) AF: 0.703 AC: 7417 AN: 10552

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48338 AN: 67952

Other (OTH) AF: 0.703 AC: 1479 AN: 2104

Alfa AF: 0.646 Hom.: 2122

Bravo AF: 0.707

Asia WGS AF: 0.548 AC: 1906 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.6
DANN	Benign	0.64
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs41835; hg19: chr7-106265565;