7-107859502-T-C

Variant names:

• chr7-107859502-T-C
• rs6947045
• ENST00000820624.1:n.150-2386A>G

Variant summary

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

The ENST00000820624.1(ENSG00000306740):​n.150-2386A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,066 control chromosomes in the GnomAD database, including 22,160 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 0.52 (22160 hom., cov: 32)
• Consequence: ENSG00000306740 ENST00000820624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 12 publications found

Genes affected

ENSG00000306740 (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 (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820624.1. 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
	ENSG00000306740	ENST00000820624.1		n.150-2386A>G		intron	N/A
	ENSG00000306740	ENST00000820625.1		n.141-2386A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79315 AN: 151950 Hom.: 22153 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.522 AC: 79329 AN: 152066 Hom.: 22160 Cov.: 32 AF XY: 0.531 AC XY: 39442 AN XY: 74328

African (AFR) AF: 0.318 AC: 13179 AN: 41484

American (AMR) AF: 0.579 AC: 8844 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3470

East Asian (EAS) AF: 0.855 AC: 4419 AN: 5168

South Asian (SAS) AF: 0.573 AC: 2763 AN: 4822

European-Finnish (FIN) AF: 0.604 AC: 6385 AN: 10570

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39611 AN: 67960

Other (OTH) AF: 0.548 AC: 1156 AN: 2110

Alfa AF: 0.533 Hom.: 9409

Bravo AF: 0.509

Asia WGS AF: 0.719 AC: 2500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.35
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs6947045; hg19: chr7-107499947;