7-135803873-A-G

Variant names:

• chr7-135803873-A-G
• rs6946494
• ENST00000419211.3:n.607+28758A>G

Variant summary

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

The ENST00000419211.3(ENSG00000224746):​n.607+28758A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,190 control chromosomes in the GnomAD database, including 1,734 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 0.15 (1734 hom., cov: 33)
• Consequence: ENSG00000224746 ENST00000419211.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236
• Publications: 6 publications found

Genes affected

ENSG00000224746 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419211.3. 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
	ENSG00000224746	ENST00000419211.3	TSL:2	n.607+28758A>G		intron	N/A
	ENSG00000224746	ENST00000830862.1		n.609+28758A>G		intron	N/A
	ENSG00000224746	ENST00000830863.1		n.615+28758A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22418 AN: 152072 Hom.: 1735 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.147 AC: 22417 AN: 152190 Hom.: 1734 Cov.: 33 AF XY: 0.143 AC XY: 10673 AN XY: 74396

African (AFR) AF: 0.130 AC: 5382 AN: 41506

American (AMR) AF: 0.114 AC: 1740 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3470

East Asian (EAS) AF: 0.112 AC: 582 AN: 5180

South Asian (SAS) AF: 0.0938 AC: 452 AN: 4818

European-Finnish (FIN) AF: 0.136 AC: 1444 AN: 10598

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11533 AN: 68010

Other (OTH) AF: 0.151 AC: 320 AN: 2116

Alfa AF: 0.161 Hom.: 7876

Bravo AF: 0.147

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.41
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6946494; hg19: chr7-135488621;