7-91604154-C-T

Variant names:

• chr7-91604154-C-T
• rs2540592
• ENST00000718159.1:n.97+39220G>A

Variant summary

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

The ENST00000718159.1(ENSG00000223665):​n.97+39220G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,044 control chromosomes in the GnomAD database, including 26,445 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 0.55 (26445 hom., cov: 32)
• Consequence: ENSG00000223665 ENST00000718159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 4 publications found

Genes affected

ENSG00000223665 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718159.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223665	ENST00000718159.1		n.97+39220G>A		intron	N/A
	ENSG00000223665	ENST00000718160.1		n.216-20769G>A		intron	N/A
	ENSG00000223665	ENST00000718161.1		n.61+39220G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83917 AN: 151926 Hom.: 26392 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.553 AC: 84023 AN: 152044 Hom.: 26445 Cov.: 32 AF XY: 0.555 AC XY: 41224 AN XY: 74318

African (AFR) AF: 0.854 AC: 35416 AN: 41482

American (AMR) AF: 0.505 AC: 7706 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1537 AN: 3470

East Asian (EAS) AF: 0.820 AC: 4242 AN: 5172

South Asian (SAS) AF: 0.604 AC: 2913 AN: 4822

European-Finnish (FIN) AF: 0.396 AC: 4179 AN: 10554

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26527 AN: 67956

Other (OTH) AF: 0.543 AC: 1146 AN: 2110

Alfa AF: 0.452 Hom.: 56241

Bravo AF: 0.574

Asia WGS AF: 0.699 AC: 2430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.13
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2540592; hg19: chr7-91233469;